From 47f7516506162b3b87b152a6260e03d3f6c538c7 Mon Sep 17 00:00:00 2001
From: faroo002 <muhammad.farooq@wur.nl>
Date: Sun, 8 Nov 2020 12:43:21 +0100
Subject: [PATCH] updated

---
 code/BLUES.R                                  |    3 -
 code/aggregate_analysis.R                     |   51 +-
 code/make_coex_features_all.R                 |  150 +-
 code/make_dataset.R                           |  222 +-
 code/make_go_features_all.R                   |  205 +-
 code/using_COEX/pla/8fold/combine.R           | 4869 +++++++++++++++++
 ...p_vs_gfblup_using_coexpression_analysis1.R |   26 +-
 code/using_COEX/psii/8fold/combine.R          | 1766 ++++++
 ...p_vs_gfblup_using_coexpression_analysis1.R |   26 +-
 code/using_COEX/run_models.R                  |   23 +-
 code/using_GO/pla/8fold/combine.R             | 3418 ++++++++++++
 code/using_GO/pla/T14_1_1001_2000.R           |   62 +-
 code/using_GO/pla/T14_1_1_1000.R              |   62 +-
 code/using_GO/pla/T14_1_2001_3000.R           |   62 +-
 code/using_GO/pla/T14_1_3001_4000.R           |   62 +-
 code/using_GO/pla/T14_1_4001_5000.R           |   62 +-
 code/using_GO/pla/T14_1_5001_6000.R           |   62 +-
 code/using_GO/pla/T14_1_6001_7297.R           |   62 +-
 code/using_GO/pla/T14_2_1001_2000.R           |   62 +-
 code/using_GO/pla/T14_2_1_1000.R              |   62 +-
 code/using_GO/pla/T14_2_2001_3000.R           |   62 +-
 code/using_GO/pla/T14_2_3001_4000.R           |   62 +-
 code/using_GO/pla/T14_2_4001_5000.R           |   62 +-
 code/using_GO/pla/T14_2_5001_6000.R           |   62 +-
 code/using_GO/pla/T14_2_6001_7297.R           |   62 +-
 code/using_GO/pla/T14_3_1001_2000.R           |   62 +-
 code/using_GO/pla/T14_3_1_1000.R              |   62 +-
 code/using_GO/pla/T14_3_2001_3000.R           |   62 +-
 code/using_GO/pla/T14_3_3001_4000.R           |   62 +-
 code/using_GO/pla/T14_3_4001_5000.R           |   62 +-
 code/using_GO/pla/T14_3_5001_6000.R           |   62 +-
 code/using_GO/pla/T14_3_6001_7297.R           |   62 +-
 code/using_GO/pla/T14_4_1001_2000.R           |   62 +-
 code/using_GO/pla/T14_4_1_1000.R              |   62 +-
 code/using_GO/pla/T14_4_2001_3000.R           |   62 +-
 code/using_GO/pla/T14_4_3001_4000.R           |   62 +-
 code/using_GO/pla/T14_4_4001_5000.R           |   62 +-
 code/using_GO/pla/T14_4_5001_6000.R           |   62 +-
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 code/using_GO/pla/T14_5_1001_2000.R           |   62 +-
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 code/using_GO/pla/T14_5_4001_5000.R           |   62 +-
 code/using_GO/pla/T14_5_5001_6000.R           |   62 +-
 code/using_GO/pla/T14_5_6001_7297.R           |   62 +-
 code/using_GO/pla/T14_6_1001_2000.R           |   62 +-
 code/using_GO/pla/T14_6_1_1000.R              |   62 +-
 code/using_GO/pla/T14_6_2001_3000.R           |   62 +-
 code/using_GO/pla/T14_6_3001_4000.R           |   62 +-
 code/using_GO/pla/T14_6_4001_5000.R           |   62 +-
 code/using_GO/pla/T14_6_5001_6000.R           |   62 +-
 code/using_GO/pla/T14_6_6001_7297.R           |   62 +-
 code/using_GO/pla/T14_7_1001_2000.R           |   62 +-
 code/using_GO/pla/T14_7_1_1000.R              |   62 +-
 code/using_GO/pla/T14_7_2001_3000.R           |   62 +-
 code/using_GO/pla/T14_7_3001_4000.R           |   62 +-
 code/using_GO/pla/T14_7_4001_5000.R           |   62 +-
 code/using_GO/pla/T14_7_5001_6000.R           |   62 +-
 code/using_GO/pla/T14_7_6001_7297.R           |   62 +-
 code/using_GO/pla/T14_8_1001_2000.R           |   62 +-
 code/using_GO/pla/T14_8_1_1000.R              |   62 +-
 code/using_GO/pla/T14_8_2001_3000.R           |   62 +-
 code/using_GO/pla/T14_8_3001_4000.R           |   62 +-
 code/using_GO/pla/T14_8_4001_5000.R           |   62 +-
 code/using_GO/pla/T14_8_5001_6000.R           |   62 +-
 code/using_GO/pla/T14_8_6001_7297.R           |   62 +-
 code/using_GO/pla/T15_1_1001_2000.R           |   62 +-
 code/using_GO/pla/T15_1_1_1000.R              |   62 +-
 code/using_GO/pla/T15_1_2001_3000.R           |   62 +-
 code/using_GO/pla/T15_1_3001_4000.R           |   62 +-
 code/using_GO/pla/T15_1_4001_5000.R           |   62 +-
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 code/using_GO/pla/T15_1_6001_7297.R           |   62 +-
 code/using_GO/pla/T15_2_1001_2000.R           |   62 +-
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 code/using_GO/pla/T15_2_2001_3000.R           |   62 +-
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 code/using_GO/pla/T15_4_2001_3000.R           |   62 +-
 code/using_GO/pla/T15_4_3001_4000.R           |   62 +-
 code/using_GO/pla/T15_4_4001_5000.R           |   62 +-
 code/using_GO/pla/T15_4_5001_6000.R           |   62 +-
 code/using_GO/pla/T15_4_6001_7297.R           |   62 +-
 code/using_GO/pla/T15_5_1001_2000.R           |   62 +-
 code/using_GO/pla/T15_5_1_1000.R              |   62 +-
 code/using_GO/pla/T15_5_2001_3000.R           |   62 +-
 code/using_GO/pla/T15_5_3001_4000.R           |   62 +-
 code/using_GO/pla/T15_5_4001_5000.R           |   62 +-
 code/using_GO/pla/T15_5_5001_6000.R           |   62 +-
 code/using_GO/pla/T15_5_6001_7297.R           |   62 +-
 code/using_GO/pla/T15_6_1001_2000.R           |   62 +-
 code/using_GO/pla/T15_6_1_1000.R              |   62 +-
 code/using_GO/pla/T15_6_2001_3000.R           |   62 +-
 code/using_GO/pla/T15_6_3001_4000.R           |   62 +-
 code/using_GO/pla/T15_6_4001_5000.R           |   62 +-
 code/using_GO/pla/T15_6_5001_6000.R           |   62 +-
 code/using_GO/pla/T15_6_6001_7297.R           |   62 +-
 code/using_GO/pla/T15_7_1001_2000.R           |   62 +-
 code/using_GO/pla/T15_7_1_1000.R              |   62 +-
 code/using_GO/pla/T15_7_2001_3000.R           |   62 +-
 code/using_GO/pla/T15_7_3001_4000.R           |   62 +-
 code/using_GO/pla/T15_7_4001_5000.R           |   62 +-
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 code/using_GO/pla/T15_7_6001_7297.R           |   62 +-
 code/using_GO/pla/T15_8_1001_2000.R           |   62 +-
 code/using_GO/pla/T15_8_1_1000.R              |   62 +-
 code/using_GO/pla/T15_8_2001_3000.R           |   62 +-
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 code/using_GO/pla/T15_8_6001_7297.R           |   62 +-
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 code/using_GO/pla/T16_1_2001_3000.R           |   62 +-
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 code/using_GO/pla/T16_1_6001_7297.R           |   62 +-
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 code/using_GO/pla/T16_2_2001_3000.R           |   62 +-
 code/using_GO/pla/T16_2_3001_4000.R           |   62 +-
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 code/using_GO/pla/T19_1_2001_3000.R           |   62 +-
 code/using_GO/pla/T19_1_3001_4000.R           |   62 +-
 code/using_GO/pla/T19_1_4001_5000.R           |   62 +-
 code/using_GO/pla/T19_1_5001_6000.R           |   62 +-
 code/using_GO/pla/T19_1_6001_7297.R           |   62 +-
 code/using_GO/pla/T19_2_1001_2000.R           |   62 +-
 code/using_GO/pla/T19_2_1_1000.R              |   62 +-
 code/using_GO/pla/T19_2_2001_3000.R           |   62 +-
 code/using_GO/pla/T19_2_3001_4000.R           |   62 +-
 code/using_GO/pla/T19_2_4001_5000.R           |   62 +-
 code/using_GO/pla/T19_2_5001_6000.R           |   62 +-
 code/using_GO/pla/T19_2_6001_7297.R           |   62 +-
 code/using_GO/pla/T19_3_1001_2000.R           |   62 +-
 code/using_GO/pla/T19_3_1_1000.R              |   62 +-
 code/using_GO/pla/T19_3_2001_3000.R           |   62 +-
 code/using_GO/pla/T19_3_3001_4000.R           |   62 +-
 code/using_GO/pla/T19_3_4001_5000.R           |   62 +-
 code/using_GO/pla/T19_3_5001_6000.R           |   62 +-
 code/using_GO/pla/T19_3_6001_7297.R           |   62 +-
 code/using_GO/pla/T19_4_1001_2000.R           |   62 +-
 code/using_GO/pla/T19_4_1_1000.R              |   62 +-
 code/using_GO/pla/T19_4_2001_3000.R           |   62 +-
 code/using_GO/pla/T19_4_3001_4000.R           |   62 +-
 code/using_GO/pla/T19_4_4001_5000.R           |   62 +-
 code/using_GO/pla/T19_4_5001_6000.R           |   62 +-
 code/using_GO/pla/T19_4_6001_7297.R           |   62 +-
 code/using_GO/pla/T19_5_1001_2000.R           |   62 +-
 code/using_GO/pla/T19_5_1_1000.R              |   62 +-
 code/using_GO/pla/T19_5_2001_3000.R           |   62 +-
 code/using_GO/pla/T19_5_3001_4000.R           |   62 +-
 code/using_GO/pla/T19_5_4001_5000.R           |   62 +-
 code/using_GO/pla/T19_5_5001_6000.R           |   62 +-
 code/using_GO/pla/T19_5_6001_7297.R           |   62 +-
 code/using_GO/pla/T19_6_1001_2000.R           |   62 +-
 code/using_GO/pla/T19_6_1_1000.R              |   62 +-
 code/using_GO/pla/T19_6_2001_3000.R           |   62 +-
 code/using_GO/pla/T19_6_3001_4000.R           |   62 +-
 code/using_GO/pla/T19_6_4001_5000.R           |   62 +-
 code/using_GO/pla/T19_6_5001_6000.R           |   62 +-
 code/using_GO/pla/T19_6_6001_7297.R           |   62 +-
 code/using_GO/pla/T19_7_1001_2000.R           |   62 +-
 code/using_GO/pla/T19_7_1_1000.R              |   62 +-
 code/using_GO/pla/T19_7_2001_3000.R           |   62 +-
 code/using_GO/pla/T19_7_3001_4000.R           |   62 +-
 code/using_GO/pla/T19_7_4001_5000.R           |   62 +-
 code/using_GO/pla/T19_7_5001_6000.R           |   62 +-
 code/using_GO/pla/T19_7_6001_7297.R           |   62 +-
 code/using_GO/pla/T19_8_1001_2000.R           |   62 +-
 code/using_GO/pla/T19_8_1_1000.R              |   62 +-
 code/using_GO/pla/T19_8_2001_3000.R           |   62 +-
 code/using_GO/pla/T19_8_3001_4000.R           |   62 +-
 code/using_GO/pla/T19_8_4001_5000.R           |   62 +-
 code/using_GO/pla/T19_8_5001_6000.R           |   62 +-
 code/using_GO/pla/T19_8_6001_7297.R           |   62 +-
 code/using_GO/pla/T20_1_1001_2000.R           |   62 +-
 code/using_GO/pla/T20_1_1_1000.R              |   62 +-
 code/using_GO/pla/T20_1_2001_3000.R           |   62 +-
 code/using_GO/pla/T20_1_3001_4000.R           |   62 +-
 code/using_GO/pla/T20_1_4001_5000.R           |   62 +-
 code/using_GO/pla/T20_1_5001_6000.R           |   62 +-
 code/using_GO/pla/T20_1_6001_7297.R           |   62 +-
 code/using_GO/pla/T20_2_1001_2000.R           |   62 +-
 code/using_GO/pla/T20_2_1_1000.R              |   62 +-
 code/using_GO/pla/T20_2_2001_3000.R           |   62 +-
 code/using_GO/pla/T20_2_3001_4000.R           |   62 +-
 code/using_GO/pla/T20_2_4001_5000.R           |   62 +-
 code/using_GO/pla/T20_2_5001_6000.R           |   62 +-
 code/using_GO/pla/T20_2_6001_7297.R           |   62 +-
 .../pla/gblup_vs_gfblup_using_go_analysis1.R  |   20 +-
 code/using_GO/psii/8fold/combine.R            | 1258 +++++
 .../psii/gblup_vs_gfblup_using_go_analysis1.R |   58 +-
 code/using_GO/run_models.R                    |   23 +-
 code/using_GO/test.R                          |   21 +
 366 files changed, 25779 insertions(+), 8060 deletions(-)
 create mode 100644 code/using_COEX/pla/8fold/combine.R
 create mode 100644 code/using_COEX/psii/8fold/combine.R
 create mode 100644 code/using_GO/pla/8fold/combine.R
 create mode 100644 code/using_GO/psii/8fold/combine.R
 create mode 100644 code/using_GO/test.R

diff --git a/code/BLUES.R b/code/BLUES.R
index c497179..9597e3c 100644
--- a/code/BLUES.R
+++ b/code/BLUES.R
@@ -1,6 +1,3 @@
-
-###B6 Script Specialized for MPI experiment August-September 2018 by Tom Theeuwen###################################
-
 library(lme4); library(lmerTest); library(pbkrtest)
 setwd('../data/')
 data <- na.omit(as.data.frame(read.table("s8.csv", sep = ",", header = TRUE)))
diff --git a/code/aggregate_analysis.R b/code/aggregate_analysis.R
index d4f8b73..98c25d1 100644
--- a/code/aggregate_analysis.R
+++ b/code/aggregate_analysis.R
@@ -47,30 +47,33 @@ library("pheatmap")
 
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 #################################################################################################################################################
-all_coexpression_clusters <-readRDS(file ="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/all_coexpression_clusters.rds")
-coex_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers_number.rds")
-coex_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers.rds")
-go_all_genes=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_all_genes.rds")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-go_GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")	#7297	excluding those go terms with zero markers
-go_rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")	#7297	excluding those go terms with zero markers	
-coex_GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/GF.rds")
-coex_rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/rGF.rds")
-go_db=read.table("/mnt/LTR_userdata/faroo002/arabidopsis/AtSNPtile1/GO_database.tbl",header=T,sep="\t")
-
-#go_coex_overlap=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap.rds")
-#go_coex_overlap_numbers=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_numbers.rds")
-#go_coex_overlap_go_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_go_percent.rds")
-#go_coex_overlap_coex_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_coex_percent.rds")
-#best_go_coex_overlaps_go_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/best_go_coex_overlaps_go_percent.rds")
-#best_go_coex_overlaps_coex_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/best_go_coex_overlaps_coex_percent.rds")
-#psii_filtered_coex_similarity_using_go=readRDS("psii_filtered_coex_similarity_using_go.tbl")
-#psii_filtered_coex_similarity_using_genes=readRDS("psii_filtered_coex_similarity_using_genes.tbl")
-#pla_filtered_coex_similarity_using_go=readRDS("pla_filtered_coex_similarity_using_go.tbl")
-#pla_filtered_coex_similarity_using_genes=readRDS("pla_filtered_coex_similarity_using_genes.tbl")
+
+
+	all_coexpression_clusters <-readRDS(file ="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/all_coexpression_clusters.rds")
+	coex_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers_number.rds")
+	coex_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers.rds")
+	go_all_genes=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_all_genes.rds")
+	go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
+	go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
+	go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
+	load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
+	go_GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")	#7297	excluding those go terms with zero markers
+	go_rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")	#7297	excluding those go terms with zero markers	
+	coex_GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/GF.rds")
+	coex_rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/rGF.rds")
+	go_db=read.table("/mnt/LTR_userdata/faroo002/arabidopsis/AtSNPtile1/GO_database.tbl",header=T,sep="\t")
+
+	#go_coex_overlap=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap.rds")
+	#go_coex_overlap_numbers=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_numbers.rds")
+	#go_coex_overlap_go_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_go_percent.rds")
+	#go_coex_overlap_coex_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_coex_percent.rds")
+	#best_go_coex_overlaps_go_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/best_go_coex_overlaps_go_percent.rds")
+	#best_go_coex_overlaps_coex_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/best_go_coex_overlaps_coex_percent.rds")
+	#psii_filtered_coex_similarity_using_go=readRDS("psii_filtered_coex_similarity_using_go.tbl")
+	#psii_filtered_coex_similarity_using_genes=readRDS("psii_filtered_coex_similarity_using_genes.tbl")
+	#pla_filtered_coex_similarity_using_go=readRDS("pla_filtered_coex_similarity_using_go.tbl")
+	#pla_filtered_coex_similarity_using_genes=readRDS("pla_filtered_coex_similarity_using_genes.tbl")
+
 #################################################################################################################################################
 #	A	L	L	D	A	T	A	
 #################################################################################################################################################
diff --git a/code/make_coex_features_all.R b/code/make_coex_features_all.R
index 4e04ad3..d14f077 100644
--- a/code/make_coex_features_all.R
+++ b/code/make_coex_features_all.R
@@ -1,4 +1,8 @@
-message("start...")
+#!/usr/bin/env Rscript
+args = commandArgs(trailingOnly=TRUE)
+
+if (length(args)==0) {rerun=FALSE;}else{rerun=args[1]}
+message("start making coex features...")
 #############################  FUNCTIONS  ##############################################
 trim <- function (x) gsub("^\\s+|\\s+$", "", x)
 `%not_in%` <- purrr::negate(`%in%`)
@@ -12,85 +16,89 @@ setwd("../data/priors/coexpression")
 library('dplyr')
 library('qgg')
 ########################################################################################
-MAC_matrix_with_header=readRDS(file="../../MAC_matrix_with_header.rds")
-accessions=readRDS(file="../../accessions.rds")
-all_nucl_genes_bed=readRDS(file="../../all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="../../ath_all_new_maf_ldpruned_map.rds")
-MAC_df=readRDS(file="../../MAC_df.rds")
-W=readRDS(file="../../W.rds")
-all_coexpression_clusters <-as.data.frame(read.table(file ="ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE))
-coex_markers_number=readRDS(file="coex_markers_number.rds")	#7432
-coex_markers=readRDS(file="coex_markers.rds")			#7432
-markerSets=readRDS(file="markerSets.rds")				
+if(rerun==FALSE)
+{
+	MAC_matrix_with_header=readRDS(file="../../MAC_matrix_with_header.rds")
+	accessions=readRDS(file="../../accessions.rds")
+	all_nucl_genes_bed=readRDS(file="../../all_nucl_genes_bed.rds")
+	ath_all_new_maf_ldpruned_map=readRDS(file="../../ath_all_new_maf_ldpruned_map.rds")
+	MAC_df=readRDS(file="../../MAC_df.rds")
+	W=readRDS(file="../../W.rds")
+	all_coexpression_clusters <-as.data.frame(read.table(file ="ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE))
+	coex_markers_number=readRDS(file="coex_markers_number.rds")	#7432
+	coex_markers=readRDS(file="coex_markers.rds")			#7432
+	markerSets=readRDS(file="markerSets.rds")	
+}else{	
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ###########################################################################################
-message("Retrieving markers for each feature")
-if(!exists("coex_markers"))
-{
-	#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-	win=0
-	gene_regions=data.frame(all_nucl_genes_bed[,1],all_nucl_genes_bed[,2]-win,all_nucl_genes_bed[,3]+win,all_nucl_genes_bed[,4],all_nucl_genes_bed[,6])
-	colnames(gene_regions)=c("chr","gstart","gend","gname","strand")
-	gene_regions[c(2,3)] <- replace(gene_regions[c(2,3)], gene_regions[c(2,3)] < 0, 0)
-	
-	coex_markers<-rep(list(list()),nrow(all_coexpression_clusters))
-	names(coex_markers)<-all_coexpression_clusters[,1]
+	message("Retrieving markers for each feature")
+	if(!exists("coex_markers"))
+	{
+		#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+		win=0
+		gene_regions=data.frame(all_nucl_genes_bed[,1],all_nucl_genes_bed[,2]-win,all_nucl_genes_bed[,3]+win,all_nucl_genes_bed[,4],all_nucl_genes_bed[,6])
+		colnames(gene_regions)=c("chr","gstart","gend","gname","strand")
+		gene_regions[c(2,3)] <- replace(gene_regions[c(2,3)], gene_regions[c(2,3)] < 0, 0)
+		
+		coex_markers<-rep(list(list()),nrow(all_coexpression_clusters))
+		names(coex_markers)<-all_coexpression_clusters[,1]
+
+		for(i in c(1:nrow(all_coexpression_clusters)))
+		{message(paste("cluster# ",i))
+				unique_lst_of_tair_ids<- as.vector(unique(unlist(as.list(strsplit(as.character(all_coexpression_clusters[i,3]),",")))))
+			coexgene_regions= gene_regions %>% filter(gname %in% unique_lst_of_tair_ids)	#some genes are missed from the list because they could not be found in the list; so I am omitting them without further investigation of the reasons...
+				mlst<-list()
+			for(j in 1:nrow(coexgene_regions))
+				{       
+				markers=ath_all_new_maf_ldpruned_map %>% filter(chr==coexgene_regions[j,1] & position >= coexgene_regions[j,2] & position<=coexgene_regions[j,3]) %>% mutate_if(is.factor, as.character)
+				mlst<-c(mlst,as.list(markers["marker_name"]))
+				}
+				coex_markers[i]<-list(unique(unlist(unname(mlst))))
+		}
+		coex_markers_number<-numeric(length=length(coex_markers))
+		for(i in c(1:length(coex_markers)))
+		{
+			coex_markers_number[i]=length(coex_markers[[i]])
+		}
+		names(coex_markers)<-all_coexpression_clusters[,1]
+		names(coex_markers_number)<-all_coexpression_clusters[,1]
 
-	for(i in c(1:nrow(all_coexpression_clusters)))
-	{message(paste("cluster# ",i))
-      		unique_lst_of_tair_ids<- as.vector(unique(unlist(as.list(strsplit(as.character(all_coexpression_clusters[i,3]),",")))))
-		coexgene_regions= gene_regions %>% filter(gname %in% unique_lst_of_tair_ids)	#some genes are missed from the list because they could not be found in the list; so I am omitting them without further investigation of the reasons...
-      		mlst<-list()
-		for(j in 1:nrow(coexgene_regions))
-      		{       
-			markers=ath_all_new_maf_ldpruned_map %>% filter(chr==coexgene_regions[j,1] & position >= coexgene_regions[j,2] & position<=coexgene_regions[j,3]) %>% mutate_if(is.factor, as.character)
-			mlst<-c(mlst,as.list(markers["marker_name"]))
-	        }
-        	coex_markers[i]<-list(unique(unlist(unname(mlst))))
+		saveRDS(coex_markers_number,"./coex_markers_number.rds")
+		saveRDS(coex_markers,"./coex_markers.rds")
 	}
-	coex_markers_number<-numeric(length=length(coex_markers))
-	for(i in c(1:length(coex_markers)))
+	###########################################################################################
+	message("Making Genomic Relationship Matrices...")
+	if(!exists("rGF"))
 	{
-		coex_markers_number[i]=length(coex_markers[[i]])
-	}
-	names(coex_markers)<-all_coexpression_clusters[,1]
-	names(coex_markers_number)<-all_coexpression_clusters[,1]
-
-	saveRDS(coex_markers_number,"./coex_markers_number.rds")
-	saveRDS(coex_markers,"./coex_markers.rds")
-}
-###########################################################################################
-message("Making Genomic Relationship Matrices...")
-if(!exists("rGF"))
-{
-  markerSets<-list()
-  for(i in c(1:length(coex_markers)))
-  {
-    if(length(coex_markers[[i]])>0)
-    {
-      markerSets=c(markerSets,coex_markers[i])
-    }
-  }
-  setsGF <- lapply(markerSets,function(x){ x[x%in%colnames(W)] })       
-  rsetsGF <- lapply(markerSets,function(x){ colnames(W)[colnames(W) %not_in% x] }) #remaining markers for each feature      
+	  markerSets<-list()
+	  for(i in c(1:length(coex_markers)))
+	  {
+		if(length(coex_markers[[i]])>0)
+		{
+		  markerSets=c(markerSets,coex_markers[i])
+		}
+	  }
+	  setsGF <- lapply(markerSets,function(x){ x[x%in%colnames(W)] })       
+	  rsetsGF <- lapply(markerSets,function(x){ colnames(W)[colnames(W) %not_in% x] }) #remaining markers for each feature      
 
-  nsets <- length(setsGF)
-  nsnps <- sapply(setsGF,length)
-  
-  #Make Genomic Relationship Matrix for each feature and its remaining markers.
-  
-  GF <- lapply(setsGF, function(x) {grm(W = W[, x])}) 
-  rGF <- lapply(rsetsGF, function(x) {grm(W = W[, x])}) 
+	  nsets <- length(setsGF)
+	  nsnps <- sapply(setsGF,length)
+	  
+	  #Make Genomic Relationship Matrix for each feature and its remaining markers.
+	  
+	  GF <- lapply(setsGF, function(x) {grm(W = W[, x])}) 
+	  rGF <- lapply(rsetsGF, function(x) {grm(W = W[, x])}) 
 
-save(markerSets,"./markerSets.rds")
-saveRDS(setsGF,"./setsGF.rds")
-saveRDS(rsetsGF,"./rsetsGF.rds")
-saveRDS(nsets,"./nsets.rds")
-saveRDS(nsnps,"./nsnps.rds")
-saveRDS(GF,"./GF.rds")
-saveRDS(rGF,"./rGF.rds")
+	save(markerSets,"./markerSets.rds")
+	saveRDS(setsGF,"./setsGF.rds")
+	saveRDS(rsetsGF,"./rsetsGF.rds")
+	saveRDS(nsets,"./nsets.rds")
+	saveRDS(nsnps,"./nsnps.rds")
+	saveRDS(GF,"./GF.rds")
+	saveRDS(rGF,"./rGF.rds")
 
 
 }
  
 ########################################################################################
+message("end of script...")]
\ No newline at end of file
diff --git a/code/make_dataset.R b/code/make_dataset.R
index f8dfb3d..442d378 100644
--- a/code/make_dataset.R
+++ b/code/make_dataset.R
@@ -1,3 +1,7 @@
+#!/usr/bin/env Rscript
+args = commandArgs(trailingOnly=TRUE)
+
+if (length(args)==0) {rerun=FALSE;}else{rerun=args[1]}
 #############################  FUNCTIONS  ##############################################
 trim <- function (x) gsub("^\\s+|\\s+$", "", x)
 `%not_in%` <- purrr::negate(`%in%`)
@@ -11,116 +15,120 @@ setwd("../data")
 library('qgg')
 library('dplyr')
 #######################################################################################
-MAC_matrix_with_header=readRDS(file="./MAC_matrix_with_header.rds")
-accessions=readRDS(file="./accessions.rds")
-all_nucl_genes_bed=readRDS(file="./all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="./ath_all_new_maf_ldpruned_map.rds")
-MAC_df=readRDS(file="./MAC_df.rds")
-W=readRDS(file="./W.rds")
+if(rerun==FALSE)
+{
+	MAC_matrix_with_header=readRDS(file="./MAC_matrix_with_header.rds")
+	accessions=readRDS(file="./accessions.rds")
+	all_nucl_genes_bed=readRDS(file="./all_nucl_genes_bed.rds")
+	ath_all_new_maf_ldpruned_map=readRDS(file="./ath_all_new_maf_ldpruned_map.rds")
+	MAC_df=readRDS(file="./MAC_df.rds")
+	W=readRDS(file="./W.rds")
 
-Pheno=readRDS(file="./Pheno.rds")
-geno_pheno=readRDS(file="./geno_pheno.rds")
-pheno_df=readRDS(file="./pheno_df.rds")
+	Pheno=readRDS(file="./Pheno.rds")
+	geno_pheno=readRDS(file="./geno_pheno.rds")
+	pheno_df=readRDS(file="./pheno_df.rds")
 
-load(file="./Pheno_pla.Rdata")
-load(file="./geno_pheno_pla.Rdata")
-load(file="./pheno_df_pla.Rdata")
-########################################################################################
-message ("loading the Markers...")
-if(!exists("MAC_matrix_with_header"))
-{
-  MAC_matrix_with_header <-as.data.frame(read.table(file ="MAC_matrix", header=TRUE, sep="",strip.white=TRUE))
-  accessions<-MAC_matrix_with_header[,1]
-  saveRDS(MAC_matrix_with_header,"MAC_matrix_with_header.rds")
-  saveRDS(accessions,"accessions.rds")
+	load(file="./Pheno_pla.Rdata")
+	load(file="./geno_pheno_pla.Rdata")
+	load(file="./pheno_df_pla.Rdata")
+}else{
+	########################################################################################
+	message ("loading the Markers...")
+	if(!exists("MAC_matrix_with_header"))
+	{
+	  MAC_matrix_with_header <-as.data.frame(read.table(file ="MAC_matrix", header=TRUE, sep="",strip.white=TRUE))
+	  accessions<-MAC_matrix_with_header[,1]
+	  saveRDS(MAC_matrix_with_header,"MAC_matrix_with_header.rds")
+	  saveRDS(accessions,"accessions.rds")
 
-}
-message ("loading the Genes List...")
-if(!exists("all_nucl_genes_bed"))
-{
-  all_nucl_genes_bed <-as.data.frame(read.table(file ="TAIR9_GFF3_only_nucl_genes.bed1", header=FALSE, sep="",strip.white=TRUE))
-  colnames(all_nucl_genes_bed)<-c("chr","start","end","name","score","strand")
-  saveRDS(all_nucl_genes_bed,"all_nucl_genes_bed.rds")
+	}
+	message ("loading the Genes List...")
+	if(!exists("all_nucl_genes_bed"))
+	{
+	  all_nucl_genes_bed <-as.data.frame(read.table(file ="TAIR9_GFF3_only_nucl_genes.bed1", header=FALSE, sep="",strip.white=TRUE))
+	  colnames(all_nucl_genes_bed)<-c("chr","start","end","name","score","strand")
+	  saveRDS(all_nucl_genes_bed,"all_nucl_genes_bed.rds")
 
-}
-message("loading the markers map")
-if(!exists("ath_all_new_maf_ldpruned_map"))
-{
-  ath_all_new_maf_ldpruned_map <-as.data.frame(read.table(file ="ath_all_new_maf_ldpruned.map", header=FALSE, sep="",strip.white=TRUE))
-  colnames(ath_all_new_maf_ldpruned_map)<-c("chr","marker_name","score","position")
-  saveRDS(ath_all_new_maf_ldpruned_map,"ath_all_new_maf_ldpruned_map.rds")
-}
-message ("loading the Phenotypes...")
-if(!exists("Pheno"))
-{
-  Pheno <-as.data.frame(read.table(file ="psii_pheno_new.tbl", header=TRUE, sep="",strip.white=TRUE))
-  saveRDS(Pheno,"Pheno.rds")
-}
+	}
+	message("loading the markers map")
+	if(!exists("ath_all_new_maf_ldpruned_map"))
+	{
+	  ath_all_new_maf_ldpruned_map <-as.data.frame(read.table(file ="ath_all_new_maf_ldpruned.map", header=FALSE, sep="",strip.white=TRUE))
+	  colnames(ath_all_new_maf_ldpruned_map)<-c("chr","marker_name","score","position")
+	  saveRDS(ath_all_new_maf_ldpruned_map,"ath_all_new_maf_ldpruned_map.rds")
+	}
+	message ("loading the Phenotypes...")
+	if(!exists("Pheno"))
+	{
+	  Pheno <-as.data.frame(read.table(file ="psii_pheno_new.tbl", header=TRUE, sep="",strip.white=TRUE))
+	  saveRDS(Pheno,"Pheno.rds")
+	}
 
-###########################################################################################
-message("Aligning genotype and phenotype data...")
-if(!exists("geno_pheno"))
-{
-  geno_pheno<-left_join(MAC_matrix_with_header,Pheno,by="accession")
-  saveRDS(geno_pheno,"geno_pheno.rds")
-}
-if(!exists("MAC_df"))
-{
-  MAC_df<-geno_pheno[,1:ncol(MAC_matrix_with_header)]
-  MAC_df<-MAC_df[,-1] #remove accessions column
-  MAC_df <- data.frame(apply(MAC_df, 2, function(x) as.numeric(as.character(x))))
-  rownames(MAC_df) <- accessions
-  saveRDS(MAC_df,file="MAC_df.rds")
-}
-if(!exists("pheno_df"))
-{
-  s<-ncol(MAC_matrix_with_header) + 1
-  pheno_df<-geno_pheno[,s:ncol(geno_pheno)]
-  pheno_df <- data.frame(apply(pheno_df, 2, function(x) as.numeric(as.character(x))))
-  rownames(pheno_df) <- accessions
-  saveRDS(pheno_df,file="pheno_df.rds")
-}
-###########################################################################################
-#Make Centered Scaled Genotypes Matrix
-message("Making W matrix...")
-if(!exists("W"))
-{
-  nMinor <- colSums(MAC_df, na.rm=TRUE)
-  nAlleles <- colSums(!is.na(MAC_df))
-  p<-nMinor/(2*nAlleles)
-  
-  W=t(MAC_df)
-  for (i in 1:length(accessions))  
-  {  
-    W[,i] <- (W[,i]-2*p)/sqrt(2*p*(1-p))
-    #isNA <- is.na(W[,i])
-    #W[isNA,i] <- 0
-  }
-  W <- t(W)
-  saveRDS(W,"W.rds")
-#-----------------------------------------------------------------------
-  #Make Genomic Relationship Matrix
-  G <- grm(W=W)
-  save(G,"G.Rdata")
+	###########################################################################################
+	message("Aligning genotype and phenotype data...")
+	if(!exists("geno_pheno"))
+	{
+	  geno_pheno<-left_join(MAC_matrix_with_header,Pheno,by="accession")
+	  saveRDS(geno_pheno,"geno_pheno.rds")
+	}
+	if(!exists("MAC_df"))
+	{
+	  MAC_df<-geno_pheno[,1:ncol(MAC_matrix_with_header)]
+	  MAC_df<-MAC_df[,-1] #remove accessions column
+	  MAC_df <- data.frame(apply(MAC_df, 2, function(x) as.numeric(as.character(x))))
+	  rownames(MAC_df) <- accessions
+	  saveRDS(MAC_df,file="MAC_df.rds")
+	}
+	if(!exists("pheno_df"))
+	{
+	  s<-ncol(MAC_matrix_with_header) + 1
+	  pheno_df<-geno_pheno[,s:ncol(geno_pheno)]
+	  pheno_df <- data.frame(apply(pheno_df, 2, function(x) as.numeric(as.character(x))))
+	  rownames(pheno_df) <- accessions
+	  saveRDS(pheno_df,file="pheno_df.rds")
+	}
+	###########################################################################################
+	#Make Centered Scaled Genotypes Matrix
+	message("Making W matrix...")
+	if(!exists("W"))
+	{
+	  nMinor <- colSums(MAC_df, na.rm=TRUE)
+	  nAlleles <- colSums(!is.na(MAC_df))
+	  p<-nMinor/(2*nAlleles)
+	  
+	  W=t(MAC_df)
+	  for (i in 1:length(accessions))  
+	  {  
+		W[,i] <- (W[,i]-2*p)/sqrt(2*p*(1-p))
+		#isNA <- is.na(W[,i])
+		#W[isNA,i] <- 0
+	  }
+	  W <- t(W)
+	  saveRDS(W,"W.rds")
+	#-----------------------------------------------------------------------
+	  #Make Genomic Relationship Matrix
+	  G <- grm(W=W)
+	  save(G,"G.Rdata")
 
-}
-###########################################################################################
-if(!exists("Pheno_pla"))
-{
-  Pheno_pla <-as.data.frame(read.table(file ="pla_blue_means.tbl", header=TRUE, sep="",strip.white=TRUE))
-  save(Pheno_pla,file="./Pheno_pla.Rdata")
-}
-message("Aligning genotype and phenotype data...")
-if(!exists("geno_pheno_pla"))
-{
-  geno_pheno_pla<-left_join(MAC_matrix_with_header,Pheno_pla,by="accession")
-  save(geno_pheno_pla,file="./geno_pheno_pla.Rdata")
-}
-if(!exists("pheno_df_pla"))
-{
-  s<-ncol(MAC_matrix_with_header) + 1
-  pheno_df_pla<-geno_pheno_pla[,s:ncol(geno_pheno_pla)]
-  pheno_df_pla <- data.frame(apply(pheno_df_pla, 2, function(x) as.numeric(as.character(x))))
-  rownames(pheno_df_pla) <- accessions
-  save(pheno_df_pla,file="./pheno_df_pla.Rdata")
-}
+	}
+	###########################################################################################
+	if(!exists("Pheno_pla"))
+	{
+	  Pheno_pla <-as.data.frame(read.table(file ="pla_blue_means.tbl", header=TRUE, sep="",strip.white=TRUE))
+	  save(Pheno_pla,file="./Pheno_pla.Rdata")
+	}
+	message("Aligning genotype and phenotype data...")
+	if(!exists("geno_pheno_pla"))
+	{
+	  geno_pheno_pla<-left_join(MAC_matrix_with_header,Pheno_pla,by="accession")
+	  save(geno_pheno_pla,file="./geno_pheno_pla.Rdata")
+	}
+	if(!exists("pheno_df_pla"))
+	{
+	  s<-ncol(MAC_matrix_with_header) + 1
+	  pheno_df_pla<-geno_pheno_pla[,s:ncol(geno_pheno_pla)]
+	  pheno_df_pla <- data.frame(apply(pheno_df_pla, 2, function(x) as.numeric(as.character(x))))
+	  rownames(pheno_df_pla) <- accessions
+	  save(pheno_df_pla,file="./pheno_df_pla.Rdata")
+	}
+}
\ No newline at end of file
diff --git a/code/make_go_features_all.R b/code/make_go_features_all.R
index e705738..acec39f 100644
--- a/code/make_go_features_all.R
+++ b/code/make_go_features_all.R
@@ -1,4 +1,8 @@
-message("start of get_go_features.R...")
+#!/usr/bin/env Rscript
+args = commandArgs(trailingOnly=TRUE)
+
+if (length(args)==0) {rerun=FALSE;}else{rerun=args[1]}
+message("Making GO based features...")
 #############################  FUNCTIONS  ##############################################
 trim <- function (x) gsub("^\\s+|\\s+$", "", x)
 `%not_in%` <- purrr::negate(`%in%`)
@@ -28,108 +32,111 @@ library('dplyr')
 library(GO.db)
 library(org.At.tair.db)
 ########################################################################################
-MAC_matrix_with_header=readRDS(file="../../MAC_matrix_with_header.rds")
-accessions=readRDS(file="../../accessions.rds")
-all_nucl_genes_bed=readRDS(file="../../all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="../../ath_all_new_maf_ldpruned_map.rds")
-Pheno=readRDS(file="../../Pheno.rds")
-geno_pheno=readRDS(file="../../geno_pheno.rds")
-MAC_df=readRDS(file="../../MAC_df.rds")
-pheno_df=readRDS(file="../../pheno_df.rds")
-W=readRDS(file="../../W.rds")
-
-go_all_genes_number=readRDS(file="go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="go_all_markers.rds")			#7432
-markerSets=readRDS(file="markerSets.rds")				#7297
-setsGF=readRDS(file="setsGF.rds")					#7297
-rsetsGF=readRDS(file="rsetsGF.rds")					#7297
-nsets=readRDS(file="nsets.rds")					#7297
-nsnps=readRDS(file="nsnps.rds")					#7297
-GF=readRDS(file="GF.rds")						#7297
-rGF=readRDS(file="rGF.rds")						#7297	
-###########################################################################################
-message("Retrieving markers for each GO")
-if(!exists("go_all_markers"))
+if(rerun==FALSE)
 {
-  go2alltair <- as.list(org.At.tairGO2ALLTAIRS)
-  go_all_markers<-rep(list(list()),length(go2alltair))
-  names(go_all_markers)<-(names(go2alltair))
-  go_all_genes_number<-numeric(length=length(go_all_markers))
 
-  if(length(go2alltair) > 0)
-  {
-    for(i in c(1:length(go2alltair)))  #Loop through all Go terms
-    {
-	message(paste("GO#",i)) 
-      	goid=names(go2alltair[i])
-      	tair_ids=go2alltair[i]
-      	lst_of_genes=list()
-      	for(j in 1:length(tair_ids[[1]])) #Loop through all Tair IDs in a GO term
-      	{
-      		lst_of_genes=c(lst_of_genes,unlist(unname(tair_ids[[1]][j])))
-      	}
-      	unique_lst_of_tair_ids<- as.vector(unique(unlist(lst_of_genes)))
-        go_all_genes_number[i]<-length(unique_lst_of_tair_ids)
-      	mlst<-list()
-      	for(j in 1:length(unique_lst_of_tair_ids))
-      	{       
-      		#for each gene find its coordinates and then find all markers in it. then append these markers to corresponding GO feature
-      		chromosome=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][1])
-      		startpos=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][2])
-      		endpos=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][3])
-      		markers=ath_all_new_maf_ldpruned_map %>% filter(chr==chromosome & position >= startpos & position<=endpos) %>% mutate_if(is.factor, as.character)
-      		#print(markers)
-      		mlst<-c(mlst,as.list(markers["marker_name"]))
-      		#print (mlst)
-        }
-        go_all_markers[i]<-list(unique(unlist(unname(mlst))))
-    }
+	MAC_matrix_with_header=readRDS(file="../../MAC_matrix_with_header.rds")
+	accessions=readRDS(file="../../accessions.rds")
+	all_nucl_genes_bed=readRDS(file="../../all_nucl_genes_bed.rds")
+	ath_all_new_maf_ldpruned_map=readRDS(file="../../ath_all_new_maf_ldpruned_map.rds")
+	Pheno=readRDS(file="../../Pheno.rds")
+	geno_pheno=readRDS(file="../../geno_pheno.rds")
+	MAC_df=readRDS(file="../../MAC_df.rds")
+	pheno_df=readRDS(file="../../pheno_df.rds")
+	W=readRDS(file="../../W.rds")
 
-    go_all_markers_number<-numeric(length=length(go_all_markers))
-    for(i in c(1:length(go_all_markers)))
-    {
-      go_all_markers_number[i]=length(go_all_markers[[i]])
-    }
-    
-  }
-  saveRDS(go_all_genes_number,"go_all_genes_number.rds")
-  saveRDS(go_all_markers_number,"go_all_markers_number.rds")
-  saveRDS(go_all_markers,"go_all_markers.rds")
-}
-###########################################################################################
-#Make Genomic Relationship Matrix for each feature and its remaining markers
-message("Making Genomic Relationship Matrices...")
-if(!exists("rGF"))
-{
-  markerSets<-list()
-  for(i in c(1:length(go_all_markers)))
-  {
-    if(length(go_all_markers[[i]])>0)
-    {
-      markerSets=c(markerSets,go_all_markers[i])
-    }
-  }
-  setsGF <- lapply(markerSets,function(x){ x[x%in%colnames(W)] })       
-  rsetsGF <- lapply(markerSets,function(x){ colnames(W)[colnames(W) %not_in% x] }) #remaining markers for each feature GO term      
+	go_all_genes_number=readRDS(file="go_all_genes_number.rds")		#7432
+	go_all_markers_number=readRDS(file="go_all_markers_number.rds")	#7432
+	go_all_markers=readRDS(file="go_all_markers.rds")			#7432
+	markerSets=readRDS(file="markerSets.rds")				#7297
+	setsGF=readRDS(file="setsGF.rds")					#7297
+	rsetsGF=readRDS(file="rsetsGF.rds")					#7297
+	nsets=readRDS(file="nsets.rds")					#7297
+	nsnps=readRDS(file="nsnps.rds")					#7297
+	GF=readRDS(file="GF.rds")						#7297
+	rGF=readRDS(file="rGF.rds")						#7297	
+}else{
+	message("Retrieving markers for each GO")
+	if(!exists("go_all_markers"))
+	{
+	  go2alltair <- as.list(org.At.tairGO2ALLTAIRS)
+	  go_all_markers<-rep(list(list()),length(go2alltair))
+	  names(go_all_markers)<-(names(go2alltair))
+	  go_all_genes_number<-numeric(length=length(go_all_markers))
 
-  nsets <- length(setsGF)
-  nsnps <- sapply(setsGF,length)
+	  if(length(go2alltair) > 0)
+	  {
+		for(i in c(1:length(go2alltair)))  #Loop through all Go terms
+		{
+		message(paste("GO#",i)) 
+			goid=names(go2alltair[i])
+			tair_ids=go2alltair[i]
+			lst_of_genes=list()
+			for(j in 1:length(tair_ids[[1]])) #Loop through all Tair IDs in a GO term
+			{
+				lst_of_genes=c(lst_of_genes,unlist(unname(tair_ids[[1]][j])))
+			}
+			unique_lst_of_tair_ids<- as.vector(unique(unlist(lst_of_genes)))
+			go_all_genes_number[i]<-length(unique_lst_of_tair_ids)
+			mlst<-list()
+			for(j in 1:length(unique_lst_of_tair_ids))
+			{       
+				#for each gene find its coordinates and then find all markers in it. then append these markers to corresponding GO feature
+				chromosome=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][1])
+				startpos=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][2])
+				endpos=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][3])
+				markers=ath_all_new_maf_ldpruned_map %>% filter(chr==chromosome & position >= startpos & position<=endpos) %>% mutate_if(is.factor, as.character)
+				#print(markers)
+				mlst<-c(mlst,as.list(markers["marker_name"]))
+				#print (mlst)
+			}
+			go_all_markers[i]<-list(unique(unlist(unname(mlst))))
+		}
 
-  saveRDS(markerSets,"markerSets.rds")
-  saveRDS(setsGF,"setsGF.rds")
-  saveRDS(rsetsGF,"rsetsGF.rds")
-  saveRDS(nsets,"nsets.rds")
-  saveRDS(nsnps,"nsnps.rds")
-  
-  #Make Genomic Relationship Matrix for each feature and its remaining markers.
-  GF <- lapply(setsGF, function(x) {grm(W = W[, x])}) 
-  saveRDS(GF,"GF.rds")
+		go_all_markers_number<-numeric(length=length(go_all_markers))
+		for(i in c(1:length(go_all_markers)))
+		{
+		  go_all_markers_number[i]=length(go_all_markers[[i]])
+		}
+		
+	  }
+	  saveRDS(go_all_genes_number,"go_all_genes_number.rds")
+	  saveRDS(go_all_markers_number,"go_all_markers_number.rds")
+	  saveRDS(go_all_markers,"go_all_markers.rds")
+	}
+	###########################################################################################
+	#Make Genomic Relationship Matrix for each feature and its remaining markers
+	message("Making Genomic Relationship Matrices...")
+	if(!exists("rGF"))
+	{
+	  markerSets<-list()
+	  for(i in c(1:length(go_all_markers)))
+	  {
+		if(length(go_all_markers[[i]])>0)
+		{
+		  markerSets=c(markerSets,go_all_markers[i])
+		}
+	  }
+	  setsGF <- lapply(markerSets,function(x){ x[x%in%colnames(W)] })       
+	  rsetsGF <- lapply(markerSets,function(x){ colnames(W)[colnames(W) %not_in% x] }) #remaining markers for each feature GO term      
 
-  rGF <- lapply(rsetsGF, function(x) {grm(W = W[, x])}) 
-  saveRDS(rGF,"rGF.rds")
+	  nsets <- length(setsGF)
+	  nsnps <- sapply(setsGF,length)
 
-}
- 
-########################################################################################
-message("end of get_go_features.R...")
+	  saveRDS(markerSets,"markerSets.rds")
+	  saveRDS(setsGF,"setsGF.rds")
+	  saveRDS(rsetsGF,"rsetsGF.rds")
+	  saveRDS(nsets,"nsets.rds")
+	  saveRDS(nsnps,"nsnps.rds")
+	  
+	  #Make Genomic Relationship Matrix for each feature and its remaining markers.
+	  GF <- lapply(setsGF, function(x) {grm(W = W[, x])}) 
+	  saveRDS(GF,"GF.rds")
+
+	  rGF <- lapply(rsetsGF, function(x) {grm(W = W[, x])}) 
+	  saveRDS(rGF,"rGF.rds")
+
+	}
+}	 
+	########################################################################################
+	message("end of script...")
diff --git a/code/using_COEX/pla/8fold/combine.R b/code/using_COEX/pla/8fold/combine.R
new file mode 100644
index 0000000..3dad55a
--- /dev/null
+++ b/code/using_COEX/pla/8fold/combine.R
@@ -0,0 +1,4869 @@
+##################################################################################################################################
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+setwd(paste0(wdir,"/",wd));
+##################################################################################################################################
+T14_1_gblup_prediction_all_1_1000=readRDS(file="T14_1_gblup_prediction_all_1_1000.rds")
+T14_1_gblup_prediction_all_1001_2000=readRDS(file="T14_1_gblup_prediction_all_1001_2000.rds")
+T14_1_gblup_prediction_all_2001_3000=readRDS(file="T14_1_gblup_prediction_all_2001_3000.rds")
+T14_1_gblup_prediction_all_3001_4000=readRDS(file="T14_1_gblup_prediction_all_3001_4000.rds")
+T14_1_gblup_prediction_all_4001_5000=readRDS(file="T14_1_gblup_prediction_all_4001_5000.rds")
+T14_1_gblup_prediction_all_5001_6000=readRDS(file="T14_1_gblup_prediction_all_5001_6000.rds")
+T14_1_gblup_prediction_all_6001_7000=readRDS(file="T14_1_gblup_prediction_all_6001_7000.rds")
+T14_1_gblup_prediction_all_7001_8000=readRDS(file="T14_1_gblup_prediction_all_7001_8000.rds")
+T14_1_gblup_prediction_all_8001_9000=readRDS(file="T14_1_gblup_prediction_all_8001_9000.rds")
+T14_1_gblup_prediction_all_9001_10000=readRDS(file="T14_1_gblup_prediction_all_9001_10000.rds")
+T14_1_gblup_prediction_all_10001_11000=readRDS(file="T14_1_gblup_prediction_all_10001_11000.rds")
+T14_1_gblup_prediction_all_11001_12419=readRDS(file="T14_1_gblup_prediction_all_11001_12419.rds")
+T14_1_gblup_prediction_all=c(T14_1_gblup_prediction_all_1_1000,T14_1_gblup_prediction_all_1001_2000,T14_1_gblup_prediction_all_2001_3000,T14_1_gblup_prediction_all_3001_4000,T14_1_gblup_prediction_all_4001_5000,T14_1_gblup_prediction_all_5001_6000,T14_1_gblup_prediction_all_6001_7000,T14_1_gblup_prediction_all_7001_8000,T14_1_gblup_prediction_all_8001_9000,T14_1_gblup_prediction_all_9001_10000,T14_1_gblup_prediction_all_10001_11000,T14_1_gblup_prediction_all_11001_12419)
+
+T14_1_gblup_variances_all_1_1000=readRDS(file="T14_1_gblup_variances_all_1_1000.rds")
+T14_1_gblup_variances_all_1001_2000=readRDS(file="T14_1_gblup_variances_all_1001_2000.rds")
+T14_1_gblup_variances_all_2001_3000=readRDS(file="T14_1_gblup_variances_all_2001_3000.rds")
+T14_1_gblup_variances_all_3001_4000=readRDS(file="T14_1_gblup_variances_all_3001_4000.rds")
+T14_1_gblup_variances_all_4001_5000=readRDS(file="T14_1_gblup_variances_all_4001_5000.rds")
+T14_1_gblup_variances_all_5001_6000=readRDS(file="T14_1_gblup_variances_all_5001_6000.rds")
+T14_1_gblup_variances_all_6001_7000=readRDS(file="T14_1_gblup_variances_all_6001_7000.rds")
+T14_1_gblup_variances_all_7001_8000=readRDS(file="T14_1_gblup_variances_all_7001_8000.rds")
+T14_1_gblup_variances_all_8001_9000=readRDS(file="T14_1_gblup_variances_all_8001_9000.rds")
+T14_1_gblup_variances_all_9001_10000=readRDS(file="T14_1_gblup_variances_all_9001_10000.rds")
+T14_1_gblup_variances_all_10001_11000=readRDS(file="T14_1_gblup_variances_all_10001_11000.rds")
+T14_1_gblup_variances_all_11001_12419=readRDS(file="T14_1_gblup_variances_all_11001_12419.rds")
+T14_1_gblup_variances_all=c(T14_1_gblup_variances_all_1_1000,T14_1_gblup_variances_all_1001_2000,T14_1_gblup_variances_all_2001_3000,T14_1_gblup_variances_all_3001_4000,T14_1_gblup_variances_all_4001_5000,T14_1_gblup_variances_all_5001_6000,T14_1_gblup_variances_all_6001_7000,T14_1_gblup_variances_all_7001_8000,T14_1_gblup_variances_all_8001_9000,T14_1_gblup_variances_all_9001_10000,T14_1_gblup_variances_all_10001_11000,T14_1_gblup_variances_all_11001_12419)
+
+saveRDS(T14_1_gblup_prediction_all,"T14_1_gblup_prediction_all.rds")
+saveRDS(T14_1_gblup_variances_all,"T14_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_1_gfblup_prediction_all_1_1000=readRDS(file="T14_1_gfblup_prediction_all_1_1000.rds")
+T14_1_gfblup_prediction_all_1001_2000=readRDS(file="T14_1_gfblup_prediction_all_1001_2000.rds")
+T14_1_gfblup_prediction_all_2001_3000=readRDS(file="T14_1_gfblup_prediction_all_2001_3000.rds")
+T14_1_gfblup_prediction_all_3001_4000=readRDS(file="T14_1_gfblup_prediction_all_3001_4000.rds")
+T14_1_gfblup_prediction_all_4001_5000=readRDS(file="T14_1_gfblup_prediction_all_4001_5000.rds")
+T14_1_gfblup_prediction_all_5001_6000=readRDS(file="T14_1_gfblup_prediction_all_5001_6000.rds")
+T14_1_gfblup_prediction_all_6001_7000=readRDS(file="T14_1_gfblup_prediction_all_6001_7000.rds")
+T14_1_gfblup_prediction_all_7001_8000=readRDS(file="T14_1_gfblup_prediction_all_7001_8000.rds")
+T14_1_gfblup_prediction_all_8001_9000=readRDS(file="T14_1_gfblup_prediction_all_8001_9000.rds")
+T14_1_gfblup_prediction_all_9001_10000=readRDS(file="T14_1_gfblup_prediction_all_9001_10000.rds")
+T14_1_gfblup_prediction_all_10001_11000=readRDS(file="T14_1_gfblup_prediction_all_10001_11000.rds")
+T14_1_gfblup_prediction_all_11001_12419=readRDS(file="T14_1_gfblup_prediction_all_11001_12419.rds")
+
+T14_1_gfblup_variances_all_1_1000=readRDS(file="T14_1_gfblup_variances_all_1_1000.rds")
+T14_1_gfblup_variances_all_1001_2000=readRDS(file="T14_1_gfblup_variances_all_1001_2000.rds")
+T14_1_gfblup_variances_all_2001_3000=readRDS(file="T14_1_gfblup_variances_all_2001_3000.rds")
+T14_1_gfblup_variances_all_3001_4000=readRDS(file="T14_1_gfblup_variances_all_3001_4000.rds")
+T14_1_gfblup_variances_all_4001_5000=readRDS(file="T14_1_gfblup_variances_all_4001_5000.rds")
+T14_1_gfblup_variances_all_5001_6000=readRDS(file="T14_1_gfblup_variances_all_5001_6000.rds")
+T14_1_gfblup_variances_all_6001_7000=readRDS(file="T14_1_gfblup_variances_all_6001_7000.rds")
+T14_1_gfblup_variances_all_7001_8000=readRDS(file="T14_1_gfblup_variances_all_7001_8000.rds")
+T14_1_gfblup_variances_all_8001_9000=readRDS(file="T14_1_gfblup_variances_all_8001_9000.rds")
+T14_1_gfblup_variances_all_9001_10000=readRDS(file="T14_1_gfblup_variances_all_9001_10000.rds")
+T14_1_gfblup_variances_all_10001_11000=readRDS(file="T14_1_gfblup_variances_all_10001_11000.rds")
+T14_1_gfblup_variances_all_11001_12419=readRDS(file="T14_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T14_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_1_gfblup_variances_all=rep(list(list()),cycles)
+T14_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_1_1000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_1001_2000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_2001_3000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_3001_4000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_4001_5000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_5001_6000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_6001_7000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_7001_8000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_8001_9000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_9001_10000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_10001_11000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_11001_12419[[r]])
+
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_1_1000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_1001_2000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_2001_3000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_3001_4000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_4001_5000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_5001_6000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_6001_7000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_7001_8000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_8001_9000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_9001_10000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_10001_11000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T14_1_gfblup_prediction_all,"T14_1_gfblup_prediction_all.rds")
+saveRDS(T14_1_gfblup_variances_all,"T14_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_2_gblup_prediction_all_1_1000=readRDS(file="T14_2_gblup_prediction_all_1_1000.rds")
+T14_2_gblup_prediction_all_1001_2000=readRDS(file="T14_2_gblup_prediction_all_1001_2000.rds")
+T14_2_gblup_prediction_all_2001_3000=readRDS(file="T14_2_gblup_prediction_all_2001_3000.rds")
+T14_2_gblup_prediction_all_3001_4000=readRDS(file="T14_2_gblup_prediction_all_3001_4000.rds")
+T14_2_gblup_prediction_all_4001_5000=readRDS(file="T14_2_gblup_prediction_all_4001_5000.rds")
+T14_2_gblup_prediction_all_5001_6000=readRDS(file="T14_2_gblup_prediction_all_5001_6000.rds")
+T14_2_gblup_prediction_all_6001_7000=readRDS(file="T14_2_gblup_prediction_all_6001_7000.rds")
+T14_2_gblup_prediction_all_7001_8000=readRDS(file="T14_2_gblup_prediction_all_7001_8000.rds")
+T14_2_gblup_prediction_all_8001_9000=readRDS(file="T14_2_gblup_prediction_all_8001_9000.rds")
+T14_2_gblup_prediction_all_9001_10000=readRDS(file="T14_2_gblup_prediction_all_9001_10000.rds")
+T14_2_gblup_prediction_all_10001_11000=readRDS(file="T14_2_gblup_prediction_all_10001_11000.rds")
+T14_2_gblup_prediction_all_11001_12419=readRDS(file="T14_2_gblup_prediction_all_11001_12419.rds")
+T14_2_gblup_prediction_all=c(T14_2_gblup_prediction_all_1_1000,T14_2_gblup_prediction_all_1001_2000,T14_2_gblup_prediction_all_2001_3000,T14_2_gblup_prediction_all_3001_4000,T14_2_gblup_prediction_all_4001_5000,T14_2_gblup_prediction_all_5001_6000,T14_2_gblup_prediction_all_6001_7000,T14_2_gblup_prediction_all_7001_8000,T14_2_gblup_prediction_all_8001_9000,T14_2_gblup_prediction_all_9001_10000,T14_2_gblup_prediction_all_10001_11000,T14_2_gblup_prediction_all_11001_12419)
+
+T14_2_gblup_variances_all_1_1000=readRDS(file="T14_2_gblup_variances_all_1_1000.rds")
+T14_2_gblup_variances_all_1001_2000=readRDS(file="T14_2_gblup_variances_all_1001_2000.rds")
+T14_2_gblup_variances_all_2001_3000=readRDS(file="T14_2_gblup_variances_all_2001_3000.rds")
+T14_2_gblup_variances_all_3001_4000=readRDS(file="T14_2_gblup_variances_all_3001_4000.rds")
+T14_2_gblup_variances_all_4001_5000=readRDS(file="T14_2_gblup_variances_all_4001_5000.rds")
+T14_2_gblup_variances_all_5001_6000=readRDS(file="T14_2_gblup_variances_all_5001_6000.rds")
+T14_2_gblup_variances_all_6001_7000=readRDS(file="T14_2_gblup_variances_all_6001_7000.rds")
+T14_2_gblup_variances_all_7001_8000=readRDS(file="T14_2_gblup_variances_all_7001_8000.rds")
+T14_2_gblup_variances_all_8001_9000=readRDS(file="T14_2_gblup_variances_all_8001_9000.rds")
+T14_2_gblup_variances_all_9001_10000=readRDS(file="T14_2_gblup_variances_all_9001_10000.rds")
+T14_2_gblup_variances_all_10001_11000=readRDS(file="T14_2_gblup_variances_all_10001_11000.rds")
+T14_2_gblup_variances_all_11001_12419=readRDS(file="T14_2_gblup_variances_all_11001_12419.rds")
+T14_2_gblup_variances_all=c(T14_2_gblup_variances_all_1_1000,T14_2_gblup_variances_all_1001_2000,T14_2_gblup_variances_all_2001_3000,T14_2_gblup_variances_all_3001_4000,T14_2_gblup_variances_all_4001_5000,T14_2_gblup_variances_all_5001_6000,T14_2_gblup_variances_all_6001_7000,T14_2_gblup_variances_all_7001_8000,T14_2_gblup_variances_all_8001_9000,T14_2_gblup_variances_all_9001_10000,T14_2_gblup_variances_all_10001_11000,T14_2_gblup_variances_all_11001_12419)
+
+saveRDS(T14_2_gblup_prediction_all,"T14_2_gblup_prediction_all.rds")
+saveRDS(T14_2_gblup_variances_all,"T14_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_2_gfblup_prediction_all_1_1000=readRDS(file="T14_2_gfblup_prediction_all_1_1000.rds")
+T14_2_gfblup_prediction_all_1001_2000=readRDS(file="T14_2_gfblup_prediction_all_1001_2000.rds")
+T14_2_gfblup_prediction_all_2001_3000=readRDS(file="T14_2_gfblup_prediction_all_2001_3000.rds")
+T14_2_gfblup_prediction_all_3001_4000=readRDS(file="T14_2_gfblup_prediction_all_3001_4000.rds")
+T14_2_gfblup_prediction_all_4001_5000=readRDS(file="T14_2_gfblup_prediction_all_4001_5000.rds")
+T14_2_gfblup_prediction_all_5001_6000=readRDS(file="T14_2_gfblup_prediction_all_5001_6000.rds")
+T14_2_gfblup_prediction_all_6001_7000=readRDS(file="T14_2_gfblup_prediction_all_6001_7000.rds")
+T14_2_gfblup_prediction_all_7001_8000=readRDS(file="T14_2_gfblup_prediction_all_7001_8000.rds")
+T14_2_gfblup_prediction_all_8001_9000=readRDS(file="T14_2_gfblup_prediction_all_8001_9000.rds")
+T14_2_gfblup_prediction_all_9001_10000=readRDS(file="T14_2_gfblup_prediction_all_9001_10000.rds")
+T14_2_gfblup_prediction_all_10001_11000=readRDS(file="T14_2_gfblup_prediction_all_10001_11000.rds")
+T14_2_gfblup_prediction_all_11001_12419=readRDS(file="T14_2_gfblup_prediction_all_11001_12419.rds")
+
+T14_2_gfblup_variances_all_1_1000=readRDS(file="T14_2_gfblup_variances_all_1_1000.rds")
+T14_2_gfblup_variances_all_1001_2000=readRDS(file="T14_2_gfblup_variances_all_1001_2000.rds")
+T14_2_gfblup_variances_all_2001_3000=readRDS(file="T14_2_gfblup_variances_all_2001_3000.rds")
+T14_2_gfblup_variances_all_3001_4000=readRDS(file="T14_2_gfblup_variances_all_3001_4000.rds")
+T14_2_gfblup_variances_all_4001_5000=readRDS(file="T14_2_gfblup_variances_all_4001_5000.rds")
+T14_2_gfblup_variances_all_5001_6000=readRDS(file="T14_2_gfblup_variances_all_5001_6000.rds")
+T14_2_gfblup_variances_all_6001_7000=readRDS(file="T14_2_gfblup_variances_all_6001_7000.rds")
+T14_2_gfblup_variances_all_7001_8000=readRDS(file="T14_2_gfblup_variances_all_7001_8000.rds")
+T14_2_gfblup_variances_all_8001_9000=readRDS(file="T14_2_gfblup_variances_all_8001_9000.rds")
+T14_2_gfblup_variances_all_9001_10000=readRDS(file="T14_2_gfblup_variances_all_9001_10000.rds")
+T14_2_gfblup_variances_all_10001_11000=readRDS(file="T14_2_gfblup_variances_all_10001_11000.rds")
+T14_2_gfblup_variances_all_11001_12419=readRDS(file="T14_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T14_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_2_gfblup_variances_all=rep(list(list()),cycles)
+T14_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_1_1000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_1001_2000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_2001_3000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_3001_4000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_4001_5000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_5001_6000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_6001_7000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_7001_8000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_8001_9000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_9001_10000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_10001_11000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_11001_12419[[r]])
+
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_1_1000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_1001_2000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_2001_3000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_3001_4000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_4001_5000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_5001_6000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_6001_7000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_7001_8000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_8001_9000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_9001_10000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_10001_11000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T14_2_gfblup_prediction_all,"T14_2_gfblup_prediction_all.rds")
+saveRDS(T14_2_gfblup_variances_all,"T14_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_3_gblup_prediction_all_1_1000=readRDS(file="T14_3_gblup_prediction_all_1_1000.rds")
+T14_3_gblup_prediction_all_1001_2000=readRDS(file="T14_3_gblup_prediction_all_1001_2000.rds")
+T14_3_gblup_prediction_all_2001_3000=readRDS(file="T14_3_gblup_prediction_all_2001_3000.rds")
+T14_3_gblup_prediction_all_3001_4000=readRDS(file="T14_3_gblup_prediction_all_3001_4000.rds")
+T14_3_gblup_prediction_all_4001_5000=readRDS(file="T14_3_gblup_prediction_all_4001_5000.rds")
+T14_3_gblup_prediction_all_5001_6000=readRDS(file="T14_3_gblup_prediction_all_5001_6000.rds")
+T14_3_gblup_prediction_all_6001_7000=readRDS(file="T14_3_gblup_prediction_all_6001_7000.rds")
+T14_3_gblup_prediction_all_7001_8000=readRDS(file="T14_3_gblup_prediction_all_7001_8000.rds")
+T14_3_gblup_prediction_all_8001_9000=readRDS(file="T14_3_gblup_prediction_all_8001_9000.rds")
+T14_3_gblup_prediction_all_9001_10000=readRDS(file="T14_3_gblup_prediction_all_9001_10000.rds")
+T14_3_gblup_prediction_all_10001_11000=readRDS(file="T14_3_gblup_prediction_all_10001_11000.rds")
+T14_3_gblup_prediction_all_11001_12419=readRDS(file="T14_3_gblup_prediction_all_11001_12419.rds")
+T14_3_gblup_prediction_all=c(T14_3_gblup_prediction_all_1_1000,T14_3_gblup_prediction_all_1001_2000,T14_3_gblup_prediction_all_2001_3000,T14_3_gblup_prediction_all_3001_4000,T14_3_gblup_prediction_all_4001_5000,T14_3_gblup_prediction_all_5001_6000,T14_3_gblup_prediction_all_6001_7000,T14_3_gblup_prediction_all_7001_8000,T14_3_gblup_prediction_all_8001_9000,T14_3_gblup_prediction_all_9001_10000,T14_3_gblup_prediction_all_10001_11000,T14_3_gblup_prediction_all_11001_12419)
+
+T14_3_gblup_variances_all_1_1000=readRDS(file="T14_3_gblup_variances_all_1_1000.rds")
+T14_3_gblup_variances_all_1001_2000=readRDS(file="T14_3_gblup_variances_all_1001_2000.rds")
+T14_3_gblup_variances_all_2001_3000=readRDS(file="T14_3_gblup_variances_all_2001_3000.rds")
+T14_3_gblup_variances_all_3001_4000=readRDS(file="T14_3_gblup_variances_all_3001_4000.rds")
+T14_3_gblup_variances_all_4001_5000=readRDS(file="T14_3_gblup_variances_all_4001_5000.rds")
+T14_3_gblup_variances_all_5001_6000=readRDS(file="T14_3_gblup_variances_all_5001_6000.rds")
+T14_3_gblup_variances_all_6001_7000=readRDS(file="T14_3_gblup_variances_all_6001_7000.rds")
+T14_3_gblup_variances_all_7001_8000=readRDS(file="T14_3_gblup_variances_all_7001_8000.rds")
+T14_3_gblup_variances_all_8001_9000=readRDS(file="T14_3_gblup_variances_all_8001_9000.rds")
+T14_3_gblup_variances_all_9001_10000=readRDS(file="T14_3_gblup_variances_all_9001_10000.rds")
+T14_3_gblup_variances_all_10001_11000=readRDS(file="T14_3_gblup_variances_all_10001_11000.rds")
+T14_3_gblup_variances_all_11001_12419=readRDS(file="T14_3_gblup_variances_all_11001_12419.rds")
+T14_3_gblup_variances_all=c(T14_3_gblup_variances_all_1_1000,T14_3_gblup_variances_all_1001_2000,T14_3_gblup_variances_all_2001_3000,T14_3_gblup_variances_all_3001_4000,T14_3_gblup_variances_all_4001_5000,T14_3_gblup_variances_all_5001_6000,T14_3_gblup_variances_all_6001_7000,T14_3_gblup_variances_all_7001_8000,T14_3_gblup_variances_all_8001_9000,T14_3_gblup_variances_all_9001_10000,T14_3_gblup_variances_all_10001_11000,T14_3_gblup_variances_all_11001_12419)
+
+saveRDS(T14_3_gblup_prediction_all,"T14_3_gblup_prediction_all.rds")
+saveRDS(T14_3_gblup_variances_all,"T14_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_3_gfblup_prediction_all_1_1000=readRDS(file="T14_3_gfblup_prediction_all_1_1000.rds")
+T14_3_gfblup_prediction_all_1001_2000=readRDS(file="T14_3_gfblup_prediction_all_1001_2000.rds")
+T14_3_gfblup_prediction_all_2001_3000=readRDS(file="T14_3_gfblup_prediction_all_2001_3000.rds")
+T14_3_gfblup_prediction_all_3001_4000=readRDS(file="T14_3_gfblup_prediction_all_3001_4000.rds")
+T14_3_gfblup_prediction_all_4001_5000=readRDS(file="T14_3_gfblup_prediction_all_4001_5000.rds")
+T14_3_gfblup_prediction_all_5001_6000=readRDS(file="T14_3_gfblup_prediction_all_5001_6000.rds")
+T14_3_gfblup_prediction_all_6001_7000=readRDS(file="T14_3_gfblup_prediction_all_6001_7000.rds")
+T14_3_gfblup_prediction_all_7001_8000=readRDS(file="T14_3_gfblup_prediction_all_7001_8000.rds")
+T14_3_gfblup_prediction_all_8001_9000=readRDS(file="T14_3_gfblup_prediction_all_8001_9000.rds")
+T14_3_gfblup_prediction_all_9001_10000=readRDS(file="T14_3_gfblup_prediction_all_9001_10000.rds")
+T14_3_gfblup_prediction_all_10001_11000=readRDS(file="T14_3_gfblup_prediction_all_10001_11000.rds")
+T14_3_gfblup_prediction_all_11001_12419=readRDS(file="T14_3_gfblup_prediction_all_11001_12419.rds")
+
+T14_3_gfblup_variances_all_1_1000=readRDS(file="T14_3_gfblup_variances_all_1_1000.rds")
+T14_3_gfblup_variances_all_1001_2000=readRDS(file="T14_3_gfblup_variances_all_1001_2000.rds")
+T14_3_gfblup_variances_all_2001_3000=readRDS(file="T14_3_gfblup_variances_all_2001_3000.rds")
+T14_3_gfblup_variances_all_3001_4000=readRDS(file="T14_3_gfblup_variances_all_3001_4000.rds")
+T14_3_gfblup_variances_all_4001_5000=readRDS(file="T14_3_gfblup_variances_all_4001_5000.rds")
+T14_3_gfblup_variances_all_5001_6000=readRDS(file="T14_3_gfblup_variances_all_5001_6000.rds")
+T14_3_gfblup_variances_all_6001_7000=readRDS(file="T14_3_gfblup_variances_all_6001_7000.rds")
+T14_3_gfblup_variances_all_7001_8000=readRDS(file="T14_3_gfblup_variances_all_7001_8000.rds")
+T14_3_gfblup_variances_all_8001_9000=readRDS(file="T14_3_gfblup_variances_all_8001_9000.rds")
+T14_3_gfblup_variances_all_9001_10000=readRDS(file="T14_3_gfblup_variances_all_9001_10000.rds")
+T14_3_gfblup_variances_all_10001_11000=readRDS(file="T14_3_gfblup_variances_all_10001_11000.rds")
+T14_3_gfblup_variances_all_11001_12419=readRDS(file="T14_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T14_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_3_gfblup_variances_all=rep(list(list()),cycles)
+T14_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_1_1000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_1001_2000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_2001_3000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_3001_4000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_4001_5000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_5001_6000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_6001_7000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_7001_8000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_8001_9000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_9001_10000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_10001_11000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_11001_12419[[r]])
+
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_1_1000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_1001_2000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_2001_3000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_3001_4000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_4001_5000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_5001_6000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_6001_7000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_7001_8000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_8001_9000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_9001_10000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_10001_11000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T14_3_gfblup_prediction_all,"T14_3_gfblup_prediction_all.rds")
+saveRDS(T14_3_gfblup_variances_all,"T14_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_4_gblup_prediction_all_1_1000=readRDS(file="T14_4_gblup_prediction_all_1_1000.rds")
+T14_4_gblup_prediction_all_1001_2000=readRDS(file="T14_4_gblup_prediction_all_1001_2000.rds")
+T14_4_gblup_prediction_all_2001_3000=readRDS(file="T14_4_gblup_prediction_all_2001_3000.rds")
+T14_4_gblup_prediction_all_3001_4000=readRDS(file="T14_4_gblup_prediction_all_3001_4000.rds")
+T14_4_gblup_prediction_all_4001_5000=readRDS(file="T14_4_gblup_prediction_all_4001_5000.rds")
+T14_4_gblup_prediction_all_5001_6000=readRDS(file="T14_4_gblup_prediction_all_5001_6000.rds")
+T14_4_gblup_prediction_all_6001_7000=readRDS(file="T14_4_gblup_prediction_all_6001_7000.rds")
+T14_4_gblup_prediction_all_7001_8000=readRDS(file="T14_4_gblup_prediction_all_7001_8000.rds")
+T14_4_gblup_prediction_all_8001_9000=readRDS(file="T14_4_gblup_prediction_all_8001_9000.rds")
+T14_4_gblup_prediction_all_9001_10000=readRDS(file="T14_4_gblup_prediction_all_9001_10000.rds")
+T14_4_gblup_prediction_all_10001_11000=readRDS(file="T14_4_gblup_prediction_all_10001_11000.rds")
+T14_4_gblup_prediction_all_11001_12419=readRDS(file="T14_4_gblup_prediction_all_11001_12419.rds")
+T14_4_gblup_prediction_all=c(T14_4_gblup_prediction_all_1_1000,T14_4_gblup_prediction_all_1001_2000,T14_4_gblup_prediction_all_2001_3000,T14_4_gblup_prediction_all_3001_4000,T14_4_gblup_prediction_all_4001_5000,T14_4_gblup_prediction_all_5001_6000,T14_4_gblup_prediction_all_6001_7000,T14_4_gblup_prediction_all_7001_8000,T14_4_gblup_prediction_all_8001_9000,T14_4_gblup_prediction_all_9001_10000,T14_4_gblup_prediction_all_10001_11000,T14_4_gblup_prediction_all_11001_12419)
+
+T14_4_gblup_variances_all_1_1000=readRDS(file="T14_4_gblup_variances_all_1_1000.rds")
+T14_4_gblup_variances_all_1001_2000=readRDS(file="T14_4_gblup_variances_all_1001_2000.rds")
+T14_4_gblup_variances_all_2001_3000=readRDS(file="T14_4_gblup_variances_all_2001_3000.rds")
+T14_4_gblup_variances_all_3001_4000=readRDS(file="T14_4_gblup_variances_all_3001_4000.rds")
+T14_4_gblup_variances_all_4001_5000=readRDS(file="T14_4_gblup_variances_all_4001_5000.rds")
+T14_4_gblup_variances_all_5001_6000=readRDS(file="T14_4_gblup_variances_all_5001_6000.rds")
+T14_4_gblup_variances_all_6001_7000=readRDS(file="T14_4_gblup_variances_all_6001_7000.rds")
+T14_4_gblup_variances_all_7001_8000=readRDS(file="T14_4_gblup_variances_all_7001_8000.rds")
+T14_4_gblup_variances_all_8001_9000=readRDS(file="T14_4_gblup_variances_all_8001_9000.rds")
+T14_4_gblup_variances_all_9001_10000=readRDS(file="T14_4_gblup_variances_all_9001_10000.rds")
+T14_4_gblup_variances_all_10001_11000=readRDS(file="T14_4_gblup_variances_all_10001_11000.rds")
+T14_4_gblup_variances_all_11001_12419=readRDS(file="T14_4_gblup_variances_all_11001_12419.rds")
+T14_4_gblup_variances_all=c(T14_4_gblup_variances_all_1_1000,T14_4_gblup_variances_all_1001_2000,T14_4_gblup_variances_all_2001_3000,T14_4_gblup_variances_all_3001_4000,T14_4_gblup_variances_all_4001_5000,T14_4_gblup_variances_all_5001_6000,T14_4_gblup_variances_all_6001_7000,T14_4_gblup_variances_all_7001_8000,T14_4_gblup_variances_all_8001_9000,T14_4_gblup_variances_all_9001_10000,T14_4_gblup_variances_all_10001_11000,T14_4_gblup_variances_all_11001_12419)
+
+saveRDS(T14_4_gblup_prediction_all,"T14_4_gblup_prediction_all.rds")
+saveRDS(T14_4_gblup_variances_all,"T14_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_4_gfblup_prediction_all_1_1000=readRDS(file="T14_4_gfblup_prediction_all_1_1000.rds")
+T14_4_gfblup_prediction_all_1001_2000=readRDS(file="T14_4_gfblup_prediction_all_1001_2000.rds")
+T14_4_gfblup_prediction_all_2001_3000=readRDS(file="T14_4_gfblup_prediction_all_2001_3000.rds")
+T14_4_gfblup_prediction_all_3001_4000=readRDS(file="T14_4_gfblup_prediction_all_3001_4000.rds")
+T14_4_gfblup_prediction_all_4001_5000=readRDS(file="T14_4_gfblup_prediction_all_4001_5000.rds")
+T14_4_gfblup_prediction_all_5001_6000=readRDS(file="T14_4_gfblup_prediction_all_5001_6000.rds")
+T14_4_gfblup_prediction_all_6001_7000=readRDS(file="T14_4_gfblup_prediction_all_6001_7000.rds")
+T14_4_gfblup_prediction_all_7001_8000=readRDS(file="T14_4_gfblup_prediction_all_7001_8000.rds")
+T14_4_gfblup_prediction_all_8001_9000=readRDS(file="T14_4_gfblup_prediction_all_8001_9000.rds")
+T14_4_gfblup_prediction_all_9001_10000=readRDS(file="T14_4_gfblup_prediction_all_9001_10000.rds")
+T14_4_gfblup_prediction_all_10001_11000=readRDS(file="T14_4_gfblup_prediction_all_10001_11000.rds")
+T14_4_gfblup_prediction_all_11001_12419=readRDS(file="T14_4_gfblup_prediction_all_11001_12419.rds")
+
+T14_4_gfblup_variances_all_1_1000=readRDS(file="T14_4_gfblup_variances_all_1_1000.rds")
+T14_4_gfblup_variances_all_1001_2000=readRDS(file="T14_4_gfblup_variances_all_1001_2000.rds")
+T14_4_gfblup_variances_all_2001_3000=readRDS(file="T14_4_gfblup_variances_all_2001_3000.rds")
+T14_4_gfblup_variances_all_3001_4000=readRDS(file="T14_4_gfblup_variances_all_3001_4000.rds")
+T14_4_gfblup_variances_all_4001_5000=readRDS(file="T14_4_gfblup_variances_all_4001_5000.rds")
+T14_4_gfblup_variances_all_5001_6000=readRDS(file="T14_4_gfblup_variances_all_5001_6000.rds")
+T14_4_gfblup_variances_all_6001_7000=readRDS(file="T14_4_gfblup_variances_all_6001_7000.rds")
+T14_4_gfblup_variances_all_7001_8000=readRDS(file="T14_4_gfblup_variances_all_7001_8000.rds")
+T14_4_gfblup_variances_all_8001_9000=readRDS(file="T14_4_gfblup_variances_all_8001_9000.rds")
+T14_4_gfblup_variances_all_9001_10000=readRDS(file="T14_4_gfblup_variances_all_9001_10000.rds")
+T14_4_gfblup_variances_all_10001_11000=readRDS(file="T14_4_gfblup_variances_all_10001_11000.rds")
+T14_4_gfblup_variances_all_11001_12419=readRDS(file="T14_4_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T14_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_4_gfblup_variances_all=rep(list(list()),cycles)
+T14_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_1_1000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_1001_2000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_2001_3000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_3001_4000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_4001_5000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_5001_6000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_6001_7000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_7001_8000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_8001_9000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_9001_10000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_10001_11000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_11001_12419[[r]])
+
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_1_1000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_1001_2000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_2001_3000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_3001_4000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_4001_5000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_5001_6000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_6001_7000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_7001_8000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_8001_9000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_9001_10000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_10001_11000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T14_4_gfblup_prediction_all,"T14_4_gfblup_prediction_all.rds")
+saveRDS(T14_4_gfblup_variances_all,"T14_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_5_gblup_prediction_all_1_1000=readRDS(file="T14_5_gblup_prediction_all_1_1000.rds")
+T14_5_gblup_prediction_all_1001_2000=readRDS(file="T14_5_gblup_prediction_all_1001_2000.rds")
+T14_5_gblup_prediction_all_2001_3000=readRDS(file="T14_5_gblup_prediction_all_2001_3000.rds")
+T14_5_gblup_prediction_all_3001_4000=readRDS(file="T14_5_gblup_prediction_all_3001_4000.rds")
+T14_5_gblup_prediction_all_4001_5000=readRDS(file="T14_5_gblup_prediction_all_4001_5000.rds")
+T14_5_gblup_prediction_all_5001_6000=readRDS(file="T14_5_gblup_prediction_all_5001_6000.rds")
+T14_5_gblup_prediction_all_6001_7000=readRDS(file="T14_5_gblup_prediction_all_6001_7000.rds")
+T14_5_gblup_prediction_all_7001_8000=readRDS(file="T14_5_gblup_prediction_all_7001_8000.rds")
+T14_5_gblup_prediction_all_8001_9000=readRDS(file="T14_5_gblup_prediction_all_8001_9000.rds")
+T14_5_gblup_prediction_all_9001_10000=readRDS(file="T14_5_gblup_prediction_all_9001_10000.rds")
+T14_5_gblup_prediction_all_10001_11000=readRDS(file="T14_5_gblup_prediction_all_10001_11000.rds")
+T14_5_gblup_prediction_all_11001_12419=readRDS(file="T14_5_gblup_prediction_all_11001_12419.rds")
+T14_5_gblup_prediction_all=c(T14_5_gblup_prediction_all_1_1000,T14_5_gblup_prediction_all_1001_2000,T14_5_gblup_prediction_all_2001_3000,T14_5_gblup_prediction_all_3001_4000,T14_5_gblup_prediction_all_4001_5000,T14_5_gblup_prediction_all_5001_6000,T14_5_gblup_prediction_all_6001_7000,T14_5_gblup_prediction_all_7001_8000,T14_5_gblup_prediction_all_8001_9000,T14_5_gblup_prediction_all_9001_10000,T14_5_gblup_prediction_all_10001_11000,T14_5_gblup_prediction_all_11001_12419)
+
+T14_5_gblup_variances_all_1_1000=readRDS(file="T14_5_gblup_variances_all_1_1000.rds")
+T14_5_gblup_variances_all_1001_2000=readRDS(file="T14_5_gblup_variances_all_1001_2000.rds")
+T14_5_gblup_variances_all_2001_3000=readRDS(file="T14_5_gblup_variances_all_2001_3000.rds")
+T14_5_gblup_variances_all_3001_4000=readRDS(file="T14_5_gblup_variances_all_3001_4000.rds")
+T14_5_gblup_variances_all_4001_5000=readRDS(file="T14_5_gblup_variances_all_4001_5000.rds")
+T14_5_gblup_variances_all_5001_6000=readRDS(file="T14_5_gblup_variances_all_5001_6000.rds")
+T14_5_gblup_variances_all_6001_7000=readRDS(file="T14_5_gblup_variances_all_6001_7000.rds")
+T14_5_gblup_variances_all_7001_8000=readRDS(file="T14_5_gblup_variances_all_7001_8000.rds")
+T14_5_gblup_variances_all_8001_9000=readRDS(file="T14_5_gblup_variances_all_8001_9000.rds")
+T14_5_gblup_variances_all_9001_10000=readRDS(file="T14_5_gblup_variances_all_9001_10000.rds")
+T14_5_gblup_variances_all_10001_11000=readRDS(file="T14_5_gblup_variances_all_10001_11000.rds")
+T14_5_gblup_variances_all_11001_12419=readRDS(file="T14_5_gblup_variances_all_11001_12419.rds")
+T14_5_gblup_variances_all=c(T14_5_gblup_variances_all_1_1000,T14_5_gblup_variances_all_1001_2000,T14_5_gblup_variances_all_2001_3000,T14_5_gblup_variances_all_3001_4000,T14_5_gblup_variances_all_4001_5000,T14_5_gblup_variances_all_5001_6000,T14_5_gblup_variances_all_6001_7000,T14_5_gblup_variances_all_7001_8000,T14_5_gblup_variances_all_8001_9000,T14_5_gblup_variances_all_9001_10000,T14_5_gblup_variances_all_10001_11000,T14_5_gblup_variances_all_11001_12419)
+
+saveRDS(T14_5_gblup_prediction_all,"T14_5_gblup_prediction_all.rds")
+saveRDS(T14_5_gblup_variances_all,"T14_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_5_gfblup_prediction_all_1_1000=readRDS(file="T14_5_gfblup_prediction_all_1_1000.rds")
+T14_5_gfblup_prediction_all_1001_2000=readRDS(file="T14_5_gfblup_prediction_all_1001_2000.rds")
+T14_5_gfblup_prediction_all_2001_3000=readRDS(file="T14_5_gfblup_prediction_all_2001_3000.rds")
+T14_5_gfblup_prediction_all_3001_4000=readRDS(file="T14_5_gfblup_prediction_all_3001_4000.rds")
+T14_5_gfblup_prediction_all_4001_5000=readRDS(file="T14_5_gfblup_prediction_all_4001_5000.rds")
+T14_5_gfblup_prediction_all_5001_6000=readRDS(file="T14_5_gfblup_prediction_all_5001_6000.rds")
+T14_5_gfblup_prediction_all_6001_7000=readRDS(file="T14_5_gfblup_prediction_all_6001_7000.rds")
+T14_5_gfblup_prediction_all_7001_8000=readRDS(file="T14_5_gfblup_prediction_all_7001_8000.rds")
+T14_5_gfblup_prediction_all_8001_9000=readRDS(file="T14_5_gfblup_prediction_all_8001_9000.rds")
+T14_5_gfblup_prediction_all_9001_10000=readRDS(file="T14_5_gfblup_prediction_all_9001_10000.rds")
+T14_5_gfblup_prediction_all_10001_11000=readRDS(file="T14_5_gfblup_prediction_all_10001_11000.rds")
+T14_5_gfblup_prediction_all_11001_12419=readRDS(file="T14_5_gfblup_prediction_all_11001_12419.rds")
+
+T14_5_gfblup_variances_all_1_1000=readRDS(file="T14_5_gfblup_variances_all_1_1000.rds")
+T14_5_gfblup_variances_all_1001_2000=readRDS(file="T14_5_gfblup_variances_all_1001_2000.rds")
+T14_5_gfblup_variances_all_2001_3000=readRDS(file="T14_5_gfblup_variances_all_2001_3000.rds")
+T14_5_gfblup_variances_all_3001_4000=readRDS(file="T14_5_gfblup_variances_all_3001_4000.rds")
+T14_5_gfblup_variances_all_4001_5000=readRDS(file="T14_5_gfblup_variances_all_4001_5000.rds")
+T14_5_gfblup_variances_all_5001_6000=readRDS(file="T14_5_gfblup_variances_all_5001_6000.rds")
+T14_5_gfblup_variances_all_6001_7000=readRDS(file="T14_5_gfblup_variances_all_6001_7000.rds")
+T14_5_gfblup_variances_all_7001_8000=readRDS(file="T14_5_gfblup_variances_all_7001_8000.rds")
+T14_5_gfblup_variances_all_8001_9000=readRDS(file="T14_5_gfblup_variances_all_8001_9000.rds")
+T14_5_gfblup_variances_all_9001_10000=readRDS(file="T14_5_gfblup_variances_all_9001_10000.rds")
+T14_5_gfblup_variances_all_10001_11000=readRDS(file="T14_5_gfblup_variances_all_10001_11000.rds")
+T14_5_gfblup_variances_all_11001_12419=readRDS(file="T14_5_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T14_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_5_gfblup_variances_all=rep(list(list()),cycles)
+T14_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_1_1000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_1001_2000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_2001_3000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_3001_4000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_4001_5000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_5001_6000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_6001_7000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_7001_8000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_8001_9000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_9001_10000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_10001_11000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_11001_12419[[r]])
+
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_1_1000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_1001_2000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_2001_3000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_3001_4000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_4001_5000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_5001_6000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_6001_7000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_7001_8000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_8001_9000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_9001_10000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_10001_11000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T14_5_gfblup_prediction_all,"T14_5_gfblup_prediction_all.rds")
+saveRDS(T14_5_gfblup_variances_all,"T14_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_6_gblup_prediction_all_1_1000=readRDS(file="T14_6_gblup_prediction_all_1_1000.rds")
+T14_6_gblup_prediction_all_1001_2000=readRDS(file="T14_6_gblup_prediction_all_1001_2000.rds")
+T14_6_gblup_prediction_all_2001_3000=readRDS(file="T14_6_gblup_prediction_all_2001_3000.rds")
+T14_6_gblup_prediction_all_3001_4000=readRDS(file="T14_6_gblup_prediction_all_3001_4000.rds")
+T14_6_gblup_prediction_all_4001_5000=readRDS(file="T14_6_gblup_prediction_all_4001_5000.rds")
+T14_6_gblup_prediction_all_5001_6000=readRDS(file="T14_6_gblup_prediction_all_5001_6000.rds")
+T14_6_gblup_prediction_all_6001_7000=readRDS(file="T14_6_gblup_prediction_all_6001_7000.rds")
+T14_6_gblup_prediction_all_7001_8000=readRDS(file="T14_6_gblup_prediction_all_7001_8000.rds")
+T14_6_gblup_prediction_all_8001_9000=readRDS(file="T14_6_gblup_prediction_all_8001_9000.rds")
+T14_6_gblup_prediction_all_9001_10000=readRDS(file="T14_6_gblup_prediction_all_9001_10000.rds")
+T14_6_gblup_prediction_all_10001_11000=readRDS(file="T14_6_gblup_prediction_all_10001_11000.rds")
+T14_6_gblup_prediction_all_11001_12419=readRDS(file="T14_6_gblup_prediction_all_11001_12419.rds")
+T14_6_gblup_prediction_all=c(T14_6_gblup_prediction_all_1_1000,T14_6_gblup_prediction_all_1001_2000,T14_6_gblup_prediction_all_2001_3000,T14_6_gblup_prediction_all_3001_4000,T14_6_gblup_prediction_all_4001_5000,T14_6_gblup_prediction_all_5001_6000,T14_6_gblup_prediction_all_6001_7000,T14_6_gblup_prediction_all_7001_8000,T14_6_gblup_prediction_all_8001_9000,T14_6_gblup_prediction_all_9001_10000,T14_6_gblup_prediction_all_10001_11000,T14_6_gblup_prediction_all_11001_12419)
+
+T14_6_gblup_variances_all_1_1000=readRDS(file="T14_6_gblup_variances_all_1_1000.rds")
+T14_6_gblup_variances_all_1001_2000=readRDS(file="T14_6_gblup_variances_all_1001_2000.rds")
+T14_6_gblup_variances_all_2001_3000=readRDS(file="T14_6_gblup_variances_all_2001_3000.rds")
+T14_6_gblup_variances_all_3001_4000=readRDS(file="T14_6_gblup_variances_all_3001_4000.rds")
+T14_6_gblup_variances_all_4001_5000=readRDS(file="T14_6_gblup_variances_all_4001_5000.rds")
+T14_6_gblup_variances_all_5001_6000=readRDS(file="T14_6_gblup_variances_all_5001_6000.rds")
+T14_6_gblup_variances_all_6001_7000=readRDS(file="T14_6_gblup_variances_all_6001_7000.rds")
+T14_6_gblup_variances_all_7001_8000=readRDS(file="T14_6_gblup_variances_all_7001_8000.rds")
+T14_6_gblup_variances_all_8001_9000=readRDS(file="T14_6_gblup_variances_all_8001_9000.rds")
+T14_6_gblup_variances_all_9001_10000=readRDS(file="T14_6_gblup_variances_all_9001_10000.rds")
+T14_6_gblup_variances_all_10001_11000=readRDS(file="T14_6_gblup_variances_all_10001_11000.rds")
+T14_6_gblup_variances_all_11001_12419=readRDS(file="T14_6_gblup_variances_all_11001_12419.rds")
+T14_6_gblup_variances_all=c(T14_6_gblup_variances_all_1_1000,T14_6_gblup_variances_all_1001_2000,T14_6_gblup_variances_all_2001_3000,T14_6_gblup_variances_all_3001_4000,T14_6_gblup_variances_all_4001_5000,T14_6_gblup_variances_all_5001_6000,T14_6_gblup_variances_all_6001_7000,T14_6_gblup_variances_all_7001_8000,T14_6_gblup_variances_all_8001_9000,T14_6_gblup_variances_all_9001_10000,T14_6_gblup_variances_all_10001_11000,T14_6_gblup_variances_all_11001_12419)
+
+saveRDS(T14_6_gblup_prediction_all,"T14_6_gblup_prediction_all.rds")
+saveRDS(T14_6_gblup_variances_all,"T14_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_6_gfblup_prediction_all_1_1000=readRDS(file="T14_6_gfblup_prediction_all_1_1000.rds")
+T14_6_gfblup_prediction_all_1001_2000=readRDS(file="T14_6_gfblup_prediction_all_1001_2000.rds")
+T14_6_gfblup_prediction_all_2001_3000=readRDS(file="T14_6_gfblup_prediction_all_2001_3000.rds")
+T14_6_gfblup_prediction_all_3001_4000=readRDS(file="T14_6_gfblup_prediction_all_3001_4000.rds")
+T14_6_gfblup_prediction_all_4001_5000=readRDS(file="T14_6_gfblup_prediction_all_4001_5000.rds")
+T14_6_gfblup_prediction_all_5001_6000=readRDS(file="T14_6_gfblup_prediction_all_5001_6000.rds")
+T14_6_gfblup_prediction_all_6001_7000=readRDS(file="T14_6_gfblup_prediction_all_6001_7000.rds")
+T14_6_gfblup_prediction_all_7001_8000=readRDS(file="T14_6_gfblup_prediction_all_7001_8000.rds")
+T14_6_gfblup_prediction_all_8001_9000=readRDS(file="T14_6_gfblup_prediction_all_8001_9000.rds")
+T14_6_gfblup_prediction_all_9001_10000=readRDS(file="T14_6_gfblup_prediction_all_9001_10000.rds")
+T14_6_gfblup_prediction_all_10001_11000=readRDS(file="T14_6_gfblup_prediction_all_10001_11000.rds")
+T14_6_gfblup_prediction_all_11001_12419=readRDS(file="T14_6_gfblup_prediction_all_11001_12419.rds")
+
+T14_6_gfblup_variances_all_1_1000=readRDS(file="T14_6_gfblup_variances_all_1_1000.rds")
+T14_6_gfblup_variances_all_1001_2000=readRDS(file="T14_6_gfblup_variances_all_1001_2000.rds")
+T14_6_gfblup_variances_all_2001_3000=readRDS(file="T14_6_gfblup_variances_all_2001_3000.rds")
+T14_6_gfblup_variances_all_3001_4000=readRDS(file="T14_6_gfblup_variances_all_3001_4000.rds")
+T14_6_gfblup_variances_all_4001_5000=readRDS(file="T14_6_gfblup_variances_all_4001_5000.rds")
+T14_6_gfblup_variances_all_5001_6000=readRDS(file="T14_6_gfblup_variances_all_5001_6000.rds")
+T14_6_gfblup_variances_all_6001_7000=readRDS(file="T14_6_gfblup_variances_all_6001_7000.rds")
+T14_6_gfblup_variances_all_7001_8000=readRDS(file="T14_6_gfblup_variances_all_7001_8000.rds")
+T14_6_gfblup_variances_all_8001_9000=readRDS(file="T14_6_gfblup_variances_all_8001_9000.rds")
+T14_6_gfblup_variances_all_9001_10000=readRDS(file="T14_6_gfblup_variances_all_9001_10000.rds")
+T14_6_gfblup_variances_all_10001_11000=readRDS(file="T14_6_gfblup_variances_all_10001_11000.rds")
+T14_6_gfblup_variances_all_11001_12419=readRDS(file="T14_6_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T14_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_6_gfblup_variances_all=rep(list(list()),cycles)
+T14_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_1_1000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_1001_2000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_2001_3000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_3001_4000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_4001_5000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_5001_6000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_6001_7000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_7001_8000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_8001_9000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_9001_10000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_10001_11000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_11001_12419[[r]])
+
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_1_1000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_1001_2000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_2001_3000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_3001_4000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_4001_5000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_5001_6000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_6001_7000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_7001_8000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_8001_9000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_9001_10000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_10001_11000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T14_6_gfblup_prediction_all,"T14_6_gfblup_prediction_all.rds")
+saveRDS(T14_6_gfblup_variances_all,"T14_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_7_gblup_prediction_all_1_1000=readRDS(file="T14_7_gblup_prediction_all_1_1000.rds")
+T14_7_gblup_prediction_all_1001_2000=readRDS(file="T14_7_gblup_prediction_all_1001_2000.rds")
+T14_7_gblup_prediction_all_2001_3000=readRDS(file="T14_7_gblup_prediction_all_2001_3000.rds")
+T14_7_gblup_prediction_all_3001_4000=readRDS(file="T14_7_gblup_prediction_all_3001_4000.rds")
+T14_7_gblup_prediction_all_4001_5000=readRDS(file="T14_7_gblup_prediction_all_4001_5000.rds")
+T14_7_gblup_prediction_all_5001_6000=readRDS(file="T14_7_gblup_prediction_all_5001_6000.rds")
+T14_7_gblup_prediction_all_6001_7000=readRDS(file="T14_7_gblup_prediction_all_6001_7000.rds")
+T14_7_gblup_prediction_all_7001_8000=readRDS(file="T14_7_gblup_prediction_all_7001_8000.rds")
+T14_7_gblup_prediction_all_8001_9000=readRDS(file="T14_7_gblup_prediction_all_8001_9000.rds")
+T14_7_gblup_prediction_all_9001_10000=readRDS(file="T14_7_gblup_prediction_all_9001_10000.rds")
+T14_7_gblup_prediction_all_10001_11000=readRDS(file="T14_7_gblup_prediction_all_10001_11000.rds")
+T14_7_gblup_prediction_all_11001_12419=readRDS(file="T14_7_gblup_prediction_all_11001_12419.rds")
+T14_7_gblup_prediction_all=c(T14_7_gblup_prediction_all_1_1000,T14_7_gblup_prediction_all_1001_2000,T14_7_gblup_prediction_all_2001_3000,T14_7_gblup_prediction_all_3001_4000,T14_7_gblup_prediction_all_4001_5000,T14_7_gblup_prediction_all_5001_6000,T14_7_gblup_prediction_all_6001_7000,T14_7_gblup_prediction_all_7001_8000,T14_7_gblup_prediction_all_8001_9000,T14_7_gblup_prediction_all_9001_10000,T14_7_gblup_prediction_all_10001_11000,T14_7_gblup_prediction_all_11001_12419)
+
+T14_7_gblup_variances_all_1_1000=readRDS(file="T14_7_gblup_variances_all_1_1000.rds")
+T14_7_gblup_variances_all_1001_2000=readRDS(file="T14_7_gblup_variances_all_1001_2000.rds")
+T14_7_gblup_variances_all_2001_3000=readRDS(file="T14_7_gblup_variances_all_2001_3000.rds")
+T14_7_gblup_variances_all_3001_4000=readRDS(file="T14_7_gblup_variances_all_3001_4000.rds")
+T14_7_gblup_variances_all_4001_5000=readRDS(file="T14_7_gblup_variances_all_4001_5000.rds")
+T14_7_gblup_variances_all_5001_6000=readRDS(file="T14_7_gblup_variances_all_5001_6000.rds")
+T14_7_gblup_variances_all_6001_7000=readRDS(file="T14_7_gblup_variances_all_6001_7000.rds")
+T14_7_gblup_variances_all_7001_8000=readRDS(file="T14_7_gblup_variances_all_7001_8000.rds")
+T14_7_gblup_variances_all_8001_9000=readRDS(file="T14_7_gblup_variances_all_8001_9000.rds")
+T14_7_gblup_variances_all_9001_10000=readRDS(file="T14_7_gblup_variances_all_9001_10000.rds")
+T14_7_gblup_variances_all_10001_11000=readRDS(file="T14_7_gblup_variances_all_10001_11000.rds")
+T14_7_gblup_variances_all_11001_12419=readRDS(file="T14_7_gblup_variances_all_11001_12419.rds")
+T14_7_gblup_variances_all=c(T14_7_gblup_variances_all_1_1000,T14_7_gblup_variances_all_1001_2000,T14_7_gblup_variances_all_2001_3000,T14_7_gblup_variances_all_3001_4000,T14_7_gblup_variances_all_4001_5000,T14_7_gblup_variances_all_5001_6000,T14_7_gblup_variances_all_6001_7000,T14_7_gblup_variances_all_7001_8000,T14_7_gblup_variances_all_8001_9000,T14_7_gblup_variances_all_9001_10000,T14_7_gblup_variances_all_10001_11000,T14_7_gblup_variances_all_11001_12419)
+
+saveRDS(T14_7_gblup_prediction_all,"T14_7_gblup_prediction_all.rds")
+saveRDS(T14_7_gblup_variances_all,"T14_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_7_gfblup_prediction_all_1_1000=readRDS(file="T14_7_gfblup_prediction_all_1_1000.rds")
+T14_7_gfblup_prediction_all_1001_2000=readRDS(file="T14_7_gfblup_prediction_all_1001_2000.rds")
+T14_7_gfblup_prediction_all_2001_3000=readRDS(file="T14_7_gfblup_prediction_all_2001_3000.rds")
+T14_7_gfblup_prediction_all_3001_4000=readRDS(file="T14_7_gfblup_prediction_all_3001_4000.rds")
+T14_7_gfblup_prediction_all_4001_5000=readRDS(file="T14_7_gfblup_prediction_all_4001_5000.rds")
+T14_7_gfblup_prediction_all_5001_6000=readRDS(file="T14_7_gfblup_prediction_all_5001_6000.rds")
+T14_7_gfblup_prediction_all_6001_7000=readRDS(file="T14_7_gfblup_prediction_all_6001_7000.rds")
+T14_7_gfblup_prediction_all_7001_8000=readRDS(file="T14_7_gfblup_prediction_all_7001_8000.rds")
+T14_7_gfblup_prediction_all_8001_9000=readRDS(file="T14_7_gfblup_prediction_all_8001_9000.rds")
+T14_7_gfblup_prediction_all_9001_10000=readRDS(file="T14_7_gfblup_prediction_all_9001_10000.rds")
+T14_7_gfblup_prediction_all_10001_11000=readRDS(file="T14_7_gfblup_prediction_all_10001_11000.rds")
+T14_7_gfblup_prediction_all_11001_12419=readRDS(file="T14_7_gfblup_prediction_all_11001_12419.rds")
+
+T14_7_gfblup_variances_all_1_1000=readRDS(file="T14_7_gfblup_variances_all_1_1000.rds")
+T14_7_gfblup_variances_all_1001_2000=readRDS(file="T14_7_gfblup_variances_all_1001_2000.rds")
+T14_7_gfblup_variances_all_2001_3000=readRDS(file="T14_7_gfblup_variances_all_2001_3000.rds")
+T14_7_gfblup_variances_all_3001_4000=readRDS(file="T14_7_gfblup_variances_all_3001_4000.rds")
+T14_7_gfblup_variances_all_4001_5000=readRDS(file="T14_7_gfblup_variances_all_4001_5000.rds")
+T14_7_gfblup_variances_all_5001_6000=readRDS(file="T14_7_gfblup_variances_all_5001_6000.rds")
+T14_7_gfblup_variances_all_6001_7000=readRDS(file="T14_7_gfblup_variances_all_6001_7000.rds")
+T14_7_gfblup_variances_all_7001_8000=readRDS(file="T14_7_gfblup_variances_all_7001_8000.rds")
+T14_7_gfblup_variances_all_8001_9000=readRDS(file="T14_7_gfblup_variances_all_8001_9000.rds")
+T14_7_gfblup_variances_all_9001_10000=readRDS(file="T14_7_gfblup_variances_all_9001_10000.rds")
+T14_7_gfblup_variances_all_10001_11000=readRDS(file="T14_7_gfblup_variances_all_10001_11000.rds")
+T14_7_gfblup_variances_all_11001_12419=readRDS(file="T14_7_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T14_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_7_gfblup_variances_all=rep(list(list()),cycles)
+T14_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_1_1000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_1001_2000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_2001_3000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_3001_4000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_4001_5000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_5001_6000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_6001_7000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_7001_8000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_8001_9000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_9001_10000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_10001_11000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_11001_12419[[r]])
+
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_1_1000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_1001_2000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_2001_3000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_3001_4000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_4001_5000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_5001_6000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_6001_7000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_7001_8000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_8001_9000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_9001_10000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_10001_11000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T14_7_gfblup_prediction_all,"T14_7_gfblup_prediction_all.rds")
+saveRDS(T14_7_gfblup_variances_all,"T14_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_8_gblup_prediction_all_1_1000=readRDS(file="T14_8_gblup_prediction_all_1_1000.rds")
+T14_8_gblup_prediction_all_1001_2000=readRDS(file="T14_8_gblup_prediction_all_1001_2000.rds")
+T14_8_gblup_prediction_all_2001_3000=readRDS(file="T14_8_gblup_prediction_all_2001_3000.rds")
+T14_8_gblup_prediction_all_3001_4000=readRDS(file="T14_8_gblup_prediction_all_3001_4000.rds")
+T14_8_gblup_prediction_all_4001_5000=readRDS(file="T14_8_gblup_prediction_all_4001_5000.rds")
+T14_8_gblup_prediction_all_5001_6000=readRDS(file="T14_8_gblup_prediction_all_5001_6000.rds")
+T14_8_gblup_prediction_all_6001_7000=readRDS(file="T14_8_gblup_prediction_all_6001_7000.rds")
+T14_8_gblup_prediction_all_7001_8000=readRDS(file="T14_8_gblup_prediction_all_7001_8000.rds")
+T14_8_gblup_prediction_all_8001_9000=readRDS(file="T14_8_gblup_prediction_all_8001_9000.rds")
+T14_8_gblup_prediction_all_9001_10000=readRDS(file="T14_8_gblup_prediction_all_9001_10000.rds")
+T14_8_gblup_prediction_all_10001_11000=readRDS(file="T14_8_gblup_prediction_all_10001_11000.rds")
+T14_8_gblup_prediction_all_11001_12419=readRDS(file="T14_8_gblup_prediction_all_11001_12419.rds")
+T14_8_gblup_prediction_all=c(T14_8_gblup_prediction_all_1_1000,T14_8_gblup_prediction_all_1001_2000,T14_8_gblup_prediction_all_2001_3000,T14_8_gblup_prediction_all_3001_4000,T14_8_gblup_prediction_all_4001_5000,T14_8_gblup_prediction_all_5001_6000,T14_8_gblup_prediction_all_6001_7000,T14_8_gblup_prediction_all_7001_8000,T14_8_gblup_prediction_all_8001_9000,T14_8_gblup_prediction_all_9001_10000,T14_8_gblup_prediction_all_10001_11000,T14_8_gblup_prediction_all_11001_12419)
+
+T14_8_gblup_variances_all_1_1000=readRDS(file="T14_8_gblup_variances_all_1_1000.rds")
+T14_8_gblup_variances_all_1001_2000=readRDS(file="T14_8_gblup_variances_all_1001_2000.rds")
+T14_8_gblup_variances_all_2001_3000=readRDS(file="T14_8_gblup_variances_all_2001_3000.rds")
+T14_8_gblup_variances_all_3001_4000=readRDS(file="T14_8_gblup_variances_all_3001_4000.rds")
+T14_8_gblup_variances_all_4001_5000=readRDS(file="T14_8_gblup_variances_all_4001_5000.rds")
+T14_8_gblup_variances_all_5001_6000=readRDS(file="T14_8_gblup_variances_all_5001_6000.rds")
+T14_8_gblup_variances_all_6001_7000=readRDS(file="T14_8_gblup_variances_all_6001_7000.rds")
+T14_8_gblup_variances_all_7001_8000=readRDS(file="T14_8_gblup_variances_all_7001_8000.rds")
+T14_8_gblup_variances_all_8001_9000=readRDS(file="T14_8_gblup_variances_all_8001_9000.rds")
+T14_8_gblup_variances_all_9001_10000=readRDS(file="T14_8_gblup_variances_all_9001_10000.rds")
+T14_8_gblup_variances_all_10001_11000=readRDS(file="T14_8_gblup_variances_all_10001_11000.rds")
+T14_8_gblup_variances_all_11001_12419=readRDS(file="T14_8_gblup_variances_all_11001_12419.rds")
+T14_8_gblup_variances_all=c(T14_8_gblup_variances_all_1_1000,T14_8_gblup_variances_all_1001_2000,T14_8_gblup_variances_all_2001_3000,T14_8_gblup_variances_all_3001_4000,T14_8_gblup_variances_all_4001_5000,T14_8_gblup_variances_all_5001_6000,T14_8_gblup_variances_all_6001_7000,T14_8_gblup_variances_all_7001_8000,T14_8_gblup_variances_all_8001_9000,T14_8_gblup_variances_all_9001_10000,T14_8_gblup_variances_all_10001_11000,T14_8_gblup_variances_all_11001_12419)
+
+saveRDS(T14_8_gblup_prediction_all,"T14_8_gblup_prediction_all.rds")
+saveRDS(T14_8_gblup_variances_all,"T14_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_8_gfblup_prediction_all_1_1000=readRDS(file="T14_8_gfblup_prediction_all_1_1000.rds")
+T14_8_gfblup_prediction_all_1001_2000=readRDS(file="T14_8_gfblup_prediction_all_1001_2000.rds")
+T14_8_gfblup_prediction_all_2001_3000=readRDS(file="T14_8_gfblup_prediction_all_2001_3000.rds")
+T14_8_gfblup_prediction_all_3001_4000=readRDS(file="T14_8_gfblup_prediction_all_3001_4000.rds")
+T14_8_gfblup_prediction_all_4001_5000=readRDS(file="T14_8_gfblup_prediction_all_4001_5000.rds")
+T14_8_gfblup_prediction_all_5001_6000=readRDS(file="T14_8_gfblup_prediction_all_5001_6000.rds")
+T14_8_gfblup_prediction_all_6001_7000=readRDS(file="T14_8_gfblup_prediction_all_6001_7000.rds")
+T14_8_gfblup_prediction_all_7001_8000=readRDS(file="T14_8_gfblup_prediction_all_7001_8000.rds")
+T14_8_gfblup_prediction_all_8001_9000=readRDS(file="T14_8_gfblup_prediction_all_8001_9000.rds")
+T14_8_gfblup_prediction_all_9001_10000=readRDS(file="T14_8_gfblup_prediction_all_9001_10000.rds")
+T14_8_gfblup_prediction_all_10001_11000=readRDS(file="T14_8_gfblup_prediction_all_10001_11000.rds")
+T14_8_gfblup_prediction_all_11001_12419=readRDS(file="T14_8_gfblup_prediction_all_11001_12419.rds")
+
+T14_8_gfblup_variances_all_1_1000=readRDS(file="T14_8_gfblup_variances_all_1_1000.rds")
+T14_8_gfblup_variances_all_1001_2000=readRDS(file="T14_8_gfblup_variances_all_1001_2000.rds")
+T14_8_gfblup_variances_all_2001_3000=readRDS(file="T14_8_gfblup_variances_all_2001_3000.rds")
+T14_8_gfblup_variances_all_3001_4000=readRDS(file="T14_8_gfblup_variances_all_3001_4000.rds")
+T14_8_gfblup_variances_all_4001_5000=readRDS(file="T14_8_gfblup_variances_all_4001_5000.rds")
+T14_8_gfblup_variances_all_5001_6000=readRDS(file="T14_8_gfblup_variances_all_5001_6000.rds")
+T14_8_gfblup_variances_all_6001_7000=readRDS(file="T14_8_gfblup_variances_all_6001_7000.rds")
+T14_8_gfblup_variances_all_7001_8000=readRDS(file="T14_8_gfblup_variances_all_7001_8000.rds")
+T14_8_gfblup_variances_all_8001_9000=readRDS(file="T14_8_gfblup_variances_all_8001_9000.rds")
+T14_8_gfblup_variances_all_9001_10000=readRDS(file="T14_8_gfblup_variances_all_9001_10000.rds")
+T14_8_gfblup_variances_all_10001_11000=readRDS(file="T14_8_gfblup_variances_all_10001_11000.rds")
+T14_8_gfblup_variances_all_11001_12419=readRDS(file="T14_8_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T14_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_8_gfblup_variances_all=rep(list(list()),cycles)
+T14_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_1_1000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_1001_2000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_2001_3000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_3001_4000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_4001_5000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_5001_6000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_6001_7000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_7001_8000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_8001_9000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_9001_10000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_10001_11000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_11001_12419[[r]])
+
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_1_1000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_1001_2000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_2001_3000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_3001_4000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_4001_5000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_5001_6000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_6001_7000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_7001_8000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_8001_9000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_9001_10000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_10001_11000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T14_8_gfblup_prediction_all,"T14_8_gfblup_prediction_all.rds")
+saveRDS(T14_8_gfblup_variances_all,"T14_8_gfblup_variances_all.rds")
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_1_gblup_prediction_all_1_1000=readRDS(file="T15_1_gblup_prediction_all_1_1000.rds")
+T15_1_gblup_prediction_all_1001_2000=readRDS(file="T15_1_gblup_prediction_all_1001_2000.rds")
+T15_1_gblup_prediction_all_2001_3000=readRDS(file="T15_1_gblup_prediction_all_2001_3000.rds")
+T15_1_gblup_prediction_all_3001_4000=readRDS(file="T15_1_gblup_prediction_all_3001_4000.rds")
+T15_1_gblup_prediction_all_4001_5000=readRDS(file="T15_1_gblup_prediction_all_4001_5000.rds")
+T15_1_gblup_prediction_all_5001_6000=readRDS(file="T15_1_gblup_prediction_all_5001_6000.rds")
+T15_1_gblup_prediction_all_6001_7000=readRDS(file="T15_1_gblup_prediction_all_6001_7000.rds")
+T15_1_gblup_prediction_all_7001_8000=readRDS(file="T15_1_gblup_prediction_all_7001_8000.rds")
+T15_1_gblup_prediction_all_8001_9000=readRDS(file="T15_1_gblup_prediction_all_8001_9000.rds")
+T15_1_gblup_prediction_all_9001_10000=readRDS(file="T15_1_gblup_prediction_all_9001_10000.rds")
+T15_1_gblup_prediction_all_10001_11000=readRDS(file="T15_1_gblup_prediction_all_10001_11000.rds")
+T15_1_gblup_prediction_all_11001_12419=readRDS(file="T15_1_gblup_prediction_all_11001_12419.rds")
+T15_1_gblup_prediction_all=c(T15_1_gblup_prediction_all_1_1000,T15_1_gblup_prediction_all_1001_2000,T15_1_gblup_prediction_all_2001_3000,T15_1_gblup_prediction_all_3001_4000,T15_1_gblup_prediction_all_4001_5000,T15_1_gblup_prediction_all_5001_6000,T15_1_gblup_prediction_all_6001_7000,T15_1_gblup_prediction_all_7001_8000,T15_1_gblup_prediction_all_8001_9000,T15_1_gblup_prediction_all_9001_10000,T15_1_gblup_prediction_all_10001_11000,T15_1_gblup_prediction_all_11001_12419)
+
+T15_1_gblup_variances_all_1_1000=readRDS(file="T15_1_gblup_variances_all_1_1000.rds")
+T15_1_gblup_variances_all_1001_2000=readRDS(file="T15_1_gblup_variances_all_1001_2000.rds")
+T15_1_gblup_variances_all_2001_3000=readRDS(file="T15_1_gblup_variances_all_2001_3000.rds")
+T15_1_gblup_variances_all_3001_4000=readRDS(file="T15_1_gblup_variances_all_3001_4000.rds")
+T15_1_gblup_variances_all_4001_5000=readRDS(file="T15_1_gblup_variances_all_4001_5000.rds")
+T15_1_gblup_variances_all_5001_6000=readRDS(file="T15_1_gblup_variances_all_5001_6000.rds")
+T15_1_gblup_variances_all_6001_7000=readRDS(file="T15_1_gblup_variances_all_6001_7000.rds")
+T15_1_gblup_variances_all_7001_8000=readRDS(file="T15_1_gblup_variances_all_7001_8000.rds")
+T15_1_gblup_variances_all_8001_9000=readRDS(file="T15_1_gblup_variances_all_8001_9000.rds")
+T15_1_gblup_variances_all_9001_10000=readRDS(file="T15_1_gblup_variances_all_9001_10000.rds")
+T15_1_gblup_variances_all_10001_11000=readRDS(file="T15_1_gblup_variances_all_10001_11000.rds")
+T15_1_gblup_variances_all_11001_12419=readRDS(file="T15_1_gblup_variances_all_11001_12419.rds")
+T15_1_gblup_variances_all=c(T15_1_gblup_variances_all_1_1000,T15_1_gblup_variances_all_1001_2000,T15_1_gblup_variances_all_2001_3000,T15_1_gblup_variances_all_3001_4000,T15_1_gblup_variances_all_4001_5000,T15_1_gblup_variances_all_5001_6000,T15_1_gblup_variances_all_6001_7000,T15_1_gblup_variances_all_7001_8000,T15_1_gblup_variances_all_8001_9000,T15_1_gblup_variances_all_9001_10000,T15_1_gblup_variances_all_10001_11000,T15_1_gblup_variances_all_11001_12419)
+
+saveRDS(T15_1_gblup_prediction_all,"T15_1_gblup_prediction_all.rds")
+saveRDS(T15_1_gblup_variances_all,"T15_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_1_gfblup_prediction_all_1_1000=readRDS(file="T15_1_gfblup_prediction_all_1_1000.rds")
+T15_1_gfblup_prediction_all_1001_2000=readRDS(file="T15_1_gfblup_prediction_all_1001_2000.rds")
+T15_1_gfblup_prediction_all_2001_3000=readRDS(file="T15_1_gfblup_prediction_all_2001_3000.rds")
+T15_1_gfblup_prediction_all_3001_4000=readRDS(file="T15_1_gfblup_prediction_all_3001_4000.rds")
+T15_1_gfblup_prediction_all_4001_5000=readRDS(file="T15_1_gfblup_prediction_all_4001_5000.rds")
+T15_1_gfblup_prediction_all_5001_6000=readRDS(file="T15_1_gfblup_prediction_all_5001_6000.rds")
+T15_1_gfblup_prediction_all_6001_7000=readRDS(file="T15_1_gfblup_prediction_all_6001_7000.rds")
+T15_1_gfblup_prediction_all_7001_8000=readRDS(file="T15_1_gfblup_prediction_all_7001_8000.rds")
+T15_1_gfblup_prediction_all_8001_9000=readRDS(file="T15_1_gfblup_prediction_all_8001_9000.rds")
+T15_1_gfblup_prediction_all_9001_10000=readRDS(file="T15_1_gfblup_prediction_all_9001_10000.rds")
+T15_1_gfblup_prediction_all_10001_11000=readRDS(file="T15_1_gfblup_prediction_all_10001_11000.rds")
+T15_1_gfblup_prediction_all_11001_12419=readRDS(file="T15_1_gfblup_prediction_all_11001_12419.rds")
+
+T15_1_gfblup_variances_all_1_1000=readRDS(file="T15_1_gfblup_variances_all_1_1000.rds")
+T15_1_gfblup_variances_all_1001_2000=readRDS(file="T15_1_gfblup_variances_all_1001_2000.rds")
+T15_1_gfblup_variances_all_2001_3000=readRDS(file="T15_1_gfblup_variances_all_2001_3000.rds")
+T15_1_gfblup_variances_all_3001_4000=readRDS(file="T15_1_gfblup_variances_all_3001_4000.rds")
+T15_1_gfblup_variances_all_4001_5000=readRDS(file="T15_1_gfblup_variances_all_4001_5000.rds")
+T15_1_gfblup_variances_all_5001_6000=readRDS(file="T15_1_gfblup_variances_all_5001_6000.rds")
+T15_1_gfblup_variances_all_6001_7000=readRDS(file="T15_1_gfblup_variances_all_6001_7000.rds")
+T15_1_gfblup_variances_all_7001_8000=readRDS(file="T15_1_gfblup_variances_all_7001_8000.rds")
+T15_1_gfblup_variances_all_8001_9000=readRDS(file="T15_1_gfblup_variances_all_8001_9000.rds")
+T15_1_gfblup_variances_all_9001_10000=readRDS(file="T15_1_gfblup_variances_all_9001_10000.rds")
+T15_1_gfblup_variances_all_10001_11000=readRDS(file="T15_1_gfblup_variances_all_10001_11000.rds")
+T15_1_gfblup_variances_all_11001_12419=readRDS(file="T15_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T15_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_1_gfblup_variances_all=rep(list(list()),cycles)
+T15_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_1_1000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_1001_2000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_2001_3000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_3001_4000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_4001_5000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_5001_6000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_6001_7000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_7001_8000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_8001_9000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_9001_10000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_10001_11000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_11001_12419[[r]])
+
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_1_1000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_1001_2000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_2001_3000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_3001_4000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_4001_5000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_5001_6000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_6001_7000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_7001_8000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_8001_9000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_9001_10000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_10001_11000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T15_1_gfblup_prediction_all,"T15_1_gfblup_prediction_all.rds")
+saveRDS(T15_1_gfblup_variances_all,"T15_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_2_gblup_prediction_all_1_1000=readRDS(file="T15_2_gblup_prediction_all_1_1000.rds")
+T15_2_gblup_prediction_all_1001_2000=readRDS(file="T15_2_gblup_prediction_all_1001_2000.rds")
+T15_2_gblup_prediction_all_2001_3000=readRDS(file="T15_2_gblup_prediction_all_2001_3000.rds")
+T15_2_gblup_prediction_all_3001_4000=readRDS(file="T15_2_gblup_prediction_all_3001_4000.rds")
+T15_2_gblup_prediction_all_4001_5000=readRDS(file="T15_2_gblup_prediction_all_4001_5000.rds")
+T15_2_gblup_prediction_all_5001_6000=readRDS(file="T15_2_gblup_prediction_all_5001_6000.rds")
+T15_2_gblup_prediction_all_6001_7000=readRDS(file="T15_2_gblup_prediction_all_6001_7000.rds")
+T15_2_gblup_prediction_all_7001_8000=readRDS(file="T15_2_gblup_prediction_all_7001_8000.rds")
+T15_2_gblup_prediction_all_8001_9000=readRDS(file="T15_2_gblup_prediction_all_8001_9000.rds")
+T15_2_gblup_prediction_all_9001_10000=readRDS(file="T15_2_gblup_prediction_all_9001_10000.rds")
+T15_2_gblup_prediction_all_10001_11000=readRDS(file="T15_2_gblup_prediction_all_10001_11000.rds")
+T15_2_gblup_prediction_all_11001_12419=readRDS(file="T15_2_gblup_prediction_all_11001_12419.rds")
+T15_2_gblup_prediction_all=c(T15_2_gblup_prediction_all_1_1000,T15_2_gblup_prediction_all_1001_2000,T15_2_gblup_prediction_all_2001_3000,T15_2_gblup_prediction_all_3001_4000,T15_2_gblup_prediction_all_4001_5000,T15_2_gblup_prediction_all_5001_6000,T15_2_gblup_prediction_all_6001_7000,T15_2_gblup_prediction_all_7001_8000,T15_2_gblup_prediction_all_8001_9000,T15_2_gblup_prediction_all_9001_10000,T15_2_gblup_prediction_all_10001_11000,T15_2_gblup_prediction_all_11001_12419)
+
+T15_2_gblup_variances_all_1_1000=readRDS(file="T15_2_gblup_variances_all_1_1000.rds")
+T15_2_gblup_variances_all_1001_2000=readRDS(file="T15_2_gblup_variances_all_1001_2000.rds")
+T15_2_gblup_variances_all_2001_3000=readRDS(file="T15_2_gblup_variances_all_2001_3000.rds")
+T15_2_gblup_variances_all_3001_4000=readRDS(file="T15_2_gblup_variances_all_3001_4000.rds")
+T15_2_gblup_variances_all_4001_5000=readRDS(file="T15_2_gblup_variances_all_4001_5000.rds")
+T15_2_gblup_variances_all_5001_6000=readRDS(file="T15_2_gblup_variances_all_5001_6000.rds")
+T15_2_gblup_variances_all_6001_7000=readRDS(file="T15_2_gblup_variances_all_6001_7000.rds")
+T15_2_gblup_variances_all_7001_8000=readRDS(file="T15_2_gblup_variances_all_7001_8000.rds")
+T15_2_gblup_variances_all_8001_9000=readRDS(file="T15_2_gblup_variances_all_8001_9000.rds")
+T15_2_gblup_variances_all_9001_10000=readRDS(file="T15_2_gblup_variances_all_9001_10000.rds")
+T15_2_gblup_variances_all_10001_11000=readRDS(file="T15_2_gblup_variances_all_10001_11000.rds")
+T15_2_gblup_variances_all_11001_12419=readRDS(file="T15_2_gblup_variances_all_11001_12419.rds")
+T15_2_gblup_variances_all=c(T15_2_gblup_variances_all_1_1000,T15_2_gblup_variances_all_1001_2000,T15_2_gblup_variances_all_2001_3000,T15_2_gblup_variances_all_3001_4000,T15_2_gblup_variances_all_4001_5000,T15_2_gblup_variances_all_5001_6000,T15_2_gblup_variances_all_6001_7000,T15_2_gblup_variances_all_7001_8000,T15_2_gblup_variances_all_8001_9000,T15_2_gblup_variances_all_9001_10000,T15_2_gblup_variances_all_10001_11000,T15_2_gblup_variances_all_11001_12419)
+
+saveRDS(T15_2_gblup_prediction_all,"T15_2_gblup_prediction_all.rds")
+saveRDS(T15_2_gblup_variances_all,"T15_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_2_gfblup_prediction_all_1_1000=readRDS(file="T15_2_gfblup_prediction_all_1_1000.rds")
+T15_2_gfblup_prediction_all_1001_2000=readRDS(file="T15_2_gfblup_prediction_all_1001_2000.rds")
+T15_2_gfblup_prediction_all_2001_3000=readRDS(file="T15_2_gfblup_prediction_all_2001_3000.rds")
+T15_2_gfblup_prediction_all_3001_4000=readRDS(file="T15_2_gfblup_prediction_all_3001_4000.rds")
+T15_2_gfblup_prediction_all_4001_5000=readRDS(file="T15_2_gfblup_prediction_all_4001_5000.rds")
+T15_2_gfblup_prediction_all_5001_6000=readRDS(file="T15_2_gfblup_prediction_all_5001_6000.rds")
+T15_2_gfblup_prediction_all_6001_7000=readRDS(file="T15_2_gfblup_prediction_all_6001_7000.rds")
+T15_2_gfblup_prediction_all_7001_8000=readRDS(file="T15_2_gfblup_prediction_all_7001_8000.rds")
+T15_2_gfblup_prediction_all_8001_9000=readRDS(file="T15_2_gfblup_prediction_all_8001_9000.rds")
+T15_2_gfblup_prediction_all_9001_10000=readRDS(file="T15_2_gfblup_prediction_all_9001_10000.rds")
+T15_2_gfblup_prediction_all_10001_11000=readRDS(file="T15_2_gfblup_prediction_all_10001_11000.rds")
+T15_2_gfblup_prediction_all_11001_12419=readRDS(file="T15_2_gfblup_prediction_all_11001_12419.rds")
+
+T15_2_gfblup_variances_all_1_1000=readRDS(file="T15_2_gfblup_variances_all_1_1000.rds")
+T15_2_gfblup_variances_all_1001_2000=readRDS(file="T15_2_gfblup_variances_all_1001_2000.rds")
+T15_2_gfblup_variances_all_2001_3000=readRDS(file="T15_2_gfblup_variances_all_2001_3000.rds")
+T15_2_gfblup_variances_all_3001_4000=readRDS(file="T15_2_gfblup_variances_all_3001_4000.rds")
+T15_2_gfblup_variances_all_4001_5000=readRDS(file="T15_2_gfblup_variances_all_4001_5000.rds")
+T15_2_gfblup_variances_all_5001_6000=readRDS(file="T15_2_gfblup_variances_all_5001_6000.rds")
+T15_2_gfblup_variances_all_6001_7000=readRDS(file="T15_2_gfblup_variances_all_6001_7000.rds")
+T15_2_gfblup_variances_all_7001_8000=readRDS(file="T15_2_gfblup_variances_all_7001_8000.rds")
+T15_2_gfblup_variances_all_8001_9000=readRDS(file="T15_2_gfblup_variances_all_8001_9000.rds")
+T15_2_gfblup_variances_all_9001_10000=readRDS(file="T15_2_gfblup_variances_all_9001_10000.rds")
+T15_2_gfblup_variances_all_10001_11000=readRDS(file="T15_2_gfblup_variances_all_10001_11000.rds")
+T15_2_gfblup_variances_all_11001_12419=readRDS(file="T15_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T15_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_2_gfblup_variances_all=rep(list(list()),cycles)
+T15_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_1_1000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_1001_2000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_2001_3000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_3001_4000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_4001_5000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_5001_6000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_6001_7000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_7001_8000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_8001_9000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_9001_10000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_10001_11000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_11001_12419[[r]])
+
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_1_1000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_1001_2000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_2001_3000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_3001_4000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_4001_5000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_5001_6000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_6001_7000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_7001_8000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_8001_9000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_9001_10000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_10001_11000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T15_2_gfblup_prediction_all,"T15_2_gfblup_prediction_all.rds")
+saveRDS(T15_2_gfblup_variances_all,"T15_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_3_gblup_prediction_all_1_1000=readRDS(file="T15_3_gblup_prediction_all_1_1000.rds")
+T15_3_gblup_prediction_all_1001_2000=readRDS(file="T15_3_gblup_prediction_all_1001_2000.rds")
+T15_3_gblup_prediction_all_2001_3000=readRDS(file="T15_3_gblup_prediction_all_2001_3000.rds")
+T15_3_gblup_prediction_all_3001_4000=readRDS(file="T15_3_gblup_prediction_all_3001_4000.rds")
+T15_3_gblup_prediction_all_4001_5000=readRDS(file="T15_3_gblup_prediction_all_4001_5000.rds")
+T15_3_gblup_prediction_all_5001_6000=readRDS(file="T15_3_gblup_prediction_all_5001_6000.rds")
+T15_3_gblup_prediction_all_6001_7000=readRDS(file="T15_3_gblup_prediction_all_6001_7000.rds")
+T15_3_gblup_prediction_all_7001_8000=readRDS(file="T15_3_gblup_prediction_all_7001_8000.rds")
+T15_3_gblup_prediction_all_8001_9000=readRDS(file="T15_3_gblup_prediction_all_8001_9000.rds")
+T15_3_gblup_prediction_all_9001_10000=readRDS(file="T15_3_gblup_prediction_all_9001_10000.rds")
+T15_3_gblup_prediction_all_10001_11000=readRDS(file="T15_3_gblup_prediction_all_10001_11000.rds")
+T15_3_gblup_prediction_all_11001_12419=readRDS(file="T15_3_gblup_prediction_all_11001_12419.rds")
+T15_3_gblup_prediction_all=c(T15_3_gblup_prediction_all_1_1000,T15_3_gblup_prediction_all_1001_2000,T15_3_gblup_prediction_all_2001_3000,T15_3_gblup_prediction_all_3001_4000,T15_3_gblup_prediction_all_4001_5000,T15_3_gblup_prediction_all_5001_6000,T15_3_gblup_prediction_all_6001_7000,T15_3_gblup_prediction_all_7001_8000,T15_3_gblup_prediction_all_8001_9000,T15_3_gblup_prediction_all_9001_10000,T15_3_gblup_prediction_all_10001_11000,T15_3_gblup_prediction_all_11001_12419)
+
+T15_3_gblup_variances_all_1_1000=readRDS(file="T15_3_gblup_variances_all_1_1000.rds")
+T15_3_gblup_variances_all_1001_2000=readRDS(file="T15_3_gblup_variances_all_1001_2000.rds")
+T15_3_gblup_variances_all_2001_3000=readRDS(file="T15_3_gblup_variances_all_2001_3000.rds")
+T15_3_gblup_variances_all_3001_4000=readRDS(file="T15_3_gblup_variances_all_3001_4000.rds")
+T15_3_gblup_variances_all_4001_5000=readRDS(file="T15_3_gblup_variances_all_4001_5000.rds")
+T15_3_gblup_variances_all_5001_6000=readRDS(file="T15_3_gblup_variances_all_5001_6000.rds")
+T15_3_gblup_variances_all_6001_7000=readRDS(file="T15_3_gblup_variances_all_6001_7000.rds")
+T15_3_gblup_variances_all_7001_8000=readRDS(file="T15_3_gblup_variances_all_7001_8000.rds")
+T15_3_gblup_variances_all_8001_9000=readRDS(file="T15_3_gblup_variances_all_8001_9000.rds")
+T15_3_gblup_variances_all_9001_10000=readRDS(file="T15_3_gblup_variances_all_9001_10000.rds")
+T15_3_gblup_variances_all_10001_11000=readRDS(file="T15_3_gblup_variances_all_10001_11000.rds")
+T15_3_gblup_variances_all_11001_12419=readRDS(file="T15_3_gblup_variances_all_11001_12419.rds")
+T15_3_gblup_variances_all=c(T15_3_gblup_variances_all_1_1000,T15_3_gblup_variances_all_1001_2000,T15_3_gblup_variances_all_2001_3000,T15_3_gblup_variances_all_3001_4000,T15_3_gblup_variances_all_4001_5000,T15_3_gblup_variances_all_5001_6000,T15_3_gblup_variances_all_6001_7000,T15_3_gblup_variances_all_7001_8000,T15_3_gblup_variances_all_8001_9000,T15_3_gblup_variances_all_9001_10000,T15_3_gblup_variances_all_10001_11000,T15_3_gblup_variances_all_11001_12419)
+
+saveRDS(T15_3_gblup_prediction_all,"T15_3_gblup_prediction_all.rds")
+saveRDS(T15_3_gblup_variances_all,"T15_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_3_gfblup_prediction_all_1_1000=readRDS(file="T15_3_gfblup_prediction_all_1_1000.rds")
+T15_3_gfblup_prediction_all_1001_2000=readRDS(file="T15_3_gfblup_prediction_all_1001_2000.rds")
+T15_3_gfblup_prediction_all_2001_3000=readRDS(file="T15_3_gfblup_prediction_all_2001_3000.rds")
+T15_3_gfblup_prediction_all_3001_4000=readRDS(file="T15_3_gfblup_prediction_all_3001_4000.rds")
+T15_3_gfblup_prediction_all_4001_5000=readRDS(file="T15_3_gfblup_prediction_all_4001_5000.rds")
+T15_3_gfblup_prediction_all_5001_6000=readRDS(file="T15_3_gfblup_prediction_all_5001_6000.rds")
+T15_3_gfblup_prediction_all_6001_7000=readRDS(file="T15_3_gfblup_prediction_all_6001_7000.rds")
+T15_3_gfblup_prediction_all_7001_8000=readRDS(file="T15_3_gfblup_prediction_all_7001_8000.rds")
+T15_3_gfblup_prediction_all_8001_9000=readRDS(file="T15_3_gfblup_prediction_all_8001_9000.rds")
+T15_3_gfblup_prediction_all_9001_10000=readRDS(file="T15_3_gfblup_prediction_all_9001_10000.rds")
+T15_3_gfblup_prediction_all_10001_11000=readRDS(file="T15_3_gfblup_prediction_all_10001_11000.rds")
+T15_3_gfblup_prediction_all_11001_12419=readRDS(file="T15_3_gfblup_prediction_all_11001_12419.rds")
+
+T15_3_gfblup_variances_all_1_1000=readRDS(file="T15_3_gfblup_variances_all_1_1000.rds")
+T15_3_gfblup_variances_all_1001_2000=readRDS(file="T15_3_gfblup_variances_all_1001_2000.rds")
+T15_3_gfblup_variances_all_2001_3000=readRDS(file="T15_3_gfblup_variances_all_2001_3000.rds")
+T15_3_gfblup_variances_all_3001_4000=readRDS(file="T15_3_gfblup_variances_all_3001_4000.rds")
+T15_3_gfblup_variances_all_4001_5000=readRDS(file="T15_3_gfblup_variances_all_4001_5000.rds")
+T15_3_gfblup_variances_all_5001_6000=readRDS(file="T15_3_gfblup_variances_all_5001_6000.rds")
+T15_3_gfblup_variances_all_6001_7000=readRDS(file="T15_3_gfblup_variances_all_6001_7000.rds")
+T15_3_gfblup_variances_all_7001_8000=readRDS(file="T15_3_gfblup_variances_all_7001_8000.rds")
+T15_3_gfblup_variances_all_8001_9000=readRDS(file="T15_3_gfblup_variances_all_8001_9000.rds")
+T15_3_gfblup_variances_all_9001_10000=readRDS(file="T15_3_gfblup_variances_all_9001_10000.rds")
+T15_3_gfblup_variances_all_10001_11000=readRDS(file="T15_3_gfblup_variances_all_10001_11000.rds")
+T15_3_gfblup_variances_all_11001_12419=readRDS(file="T15_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T15_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_3_gfblup_variances_all=rep(list(list()),cycles)
+T15_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_1_1000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_1001_2000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_2001_3000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_3001_4000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_4001_5000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_5001_6000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_6001_7000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_7001_8000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_8001_9000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_9001_10000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_10001_11000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_11001_12419[[r]])
+
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_1_1000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_1001_2000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_2001_3000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_3001_4000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_4001_5000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_5001_6000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_6001_7000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_7001_8000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_8001_9000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_9001_10000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_10001_11000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T15_3_gfblup_prediction_all,"T15_3_gfblup_prediction_all.rds")
+saveRDS(T15_3_gfblup_variances_all,"T15_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_4_gblup_prediction_all_1_1000=readRDS(file="T15_4_gblup_prediction_all_1_1000.rds")
+T15_4_gblup_prediction_all_1001_2000=readRDS(file="T15_4_gblup_prediction_all_1001_2000.rds")
+T15_4_gblup_prediction_all_2001_3000=readRDS(file="T15_4_gblup_prediction_all_2001_3000.rds")
+T15_4_gblup_prediction_all_3001_4000=readRDS(file="T15_4_gblup_prediction_all_3001_4000.rds")
+T15_4_gblup_prediction_all_4001_5000=readRDS(file="T15_4_gblup_prediction_all_4001_5000.rds")
+T15_4_gblup_prediction_all_5001_6000=readRDS(file="T15_4_gblup_prediction_all_5001_6000.rds")
+T15_4_gblup_prediction_all_6001_7000=readRDS(file="T15_4_gblup_prediction_all_6001_7000.rds")
+T15_4_gblup_prediction_all_7001_8000=readRDS(file="T15_4_gblup_prediction_all_7001_8000.rds")
+T15_4_gblup_prediction_all_8001_9000=readRDS(file="T15_4_gblup_prediction_all_8001_9000.rds")
+T15_4_gblup_prediction_all_9001_10000=readRDS(file="T15_4_gblup_prediction_all_9001_10000.rds")
+T15_4_gblup_prediction_all_10001_11000=readRDS(file="T15_4_gblup_prediction_all_10001_11000.rds")
+T15_4_gblup_prediction_all_11001_12419=readRDS(file="T15_4_gblup_prediction_all_11001_12419.rds")
+T15_4_gblup_prediction_all=c(T15_4_gblup_prediction_all_1_1000,T15_4_gblup_prediction_all_1001_2000,T15_4_gblup_prediction_all_2001_3000,T15_4_gblup_prediction_all_3001_4000,T15_4_gblup_prediction_all_4001_5000,T15_4_gblup_prediction_all_5001_6000,T15_4_gblup_prediction_all_6001_7000,T15_4_gblup_prediction_all_7001_8000,T15_4_gblup_prediction_all_8001_9000,T15_4_gblup_prediction_all_9001_10000,T15_4_gblup_prediction_all_10001_11000,T15_4_gblup_prediction_all_11001_12419)
+
+T15_4_gblup_variances_all_1_1000=readRDS(file="T15_4_gblup_variances_all_1_1000.rds")
+T15_4_gblup_variances_all_1001_2000=readRDS(file="T15_4_gblup_variances_all_1001_2000.rds")
+T15_4_gblup_variances_all_2001_3000=readRDS(file="T15_4_gblup_variances_all_2001_3000.rds")
+T15_4_gblup_variances_all_3001_4000=readRDS(file="T15_4_gblup_variances_all_3001_4000.rds")
+T15_4_gblup_variances_all_4001_5000=readRDS(file="T15_4_gblup_variances_all_4001_5000.rds")
+T15_4_gblup_variances_all_5001_6000=readRDS(file="T15_4_gblup_variances_all_5001_6000.rds")
+T15_4_gblup_variances_all_6001_7000=readRDS(file="T15_4_gblup_variances_all_6001_7000.rds")
+T15_4_gblup_variances_all_7001_8000=readRDS(file="T15_4_gblup_variances_all_7001_8000.rds")
+T15_4_gblup_variances_all_8001_9000=readRDS(file="T15_4_gblup_variances_all_8001_9000.rds")
+T15_4_gblup_variances_all_9001_10000=readRDS(file="T15_4_gblup_variances_all_9001_10000.rds")
+T15_4_gblup_variances_all_10001_11000=readRDS(file="T15_4_gblup_variances_all_10001_11000.rds")
+T15_4_gblup_variances_all_11001_12419=readRDS(file="T15_4_gblup_variances_all_11001_12419.rds")
+T15_4_gblup_variances_all=c(T15_4_gblup_variances_all_1_1000,T15_4_gblup_variances_all_1001_2000,T15_4_gblup_variances_all_2001_3000,T15_4_gblup_variances_all_3001_4000,T15_4_gblup_variances_all_4001_5000,T15_4_gblup_variances_all_5001_6000,T15_4_gblup_variances_all_6001_7000,T15_4_gblup_variances_all_7001_8000,T15_4_gblup_variances_all_8001_9000,T15_4_gblup_variances_all_9001_10000,T15_4_gblup_variances_all_10001_11000,T15_4_gblup_variances_all_11001_12419)
+
+saveRDS(T15_4_gblup_prediction_all,"T15_4_gblup_prediction_all.rds")
+saveRDS(T15_4_gblup_variances_all,"T15_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_4_gfblup_prediction_all_1_1000=readRDS(file="T15_4_gfblup_prediction_all_1_1000.rds")
+T15_4_gfblup_prediction_all_1001_2000=readRDS(file="T15_4_gfblup_prediction_all_1001_2000.rds")
+T15_4_gfblup_prediction_all_2001_3000=readRDS(file="T15_4_gfblup_prediction_all_2001_3000.rds")
+T15_4_gfblup_prediction_all_3001_4000=readRDS(file="T15_4_gfblup_prediction_all_3001_4000.rds")
+T15_4_gfblup_prediction_all_4001_5000=readRDS(file="T15_4_gfblup_prediction_all_4001_5000.rds")
+T15_4_gfblup_prediction_all_5001_6000=readRDS(file="T15_4_gfblup_prediction_all_5001_6000.rds")
+T15_4_gfblup_prediction_all_6001_7000=readRDS(file="T15_4_gfblup_prediction_all_6001_7000.rds")
+T15_4_gfblup_prediction_all_7001_8000=readRDS(file="T15_4_gfblup_prediction_all_7001_8000.rds")
+T15_4_gfblup_prediction_all_8001_9000=readRDS(file="T15_4_gfblup_prediction_all_8001_9000.rds")
+T15_4_gfblup_prediction_all_9001_10000=readRDS(file="T15_4_gfblup_prediction_all_9001_10000.rds")
+T15_4_gfblup_prediction_all_10001_11000=readRDS(file="T15_4_gfblup_prediction_all_10001_11000.rds")
+T15_4_gfblup_prediction_all_11001_12419=readRDS(file="T15_4_gfblup_prediction_all_11001_12419.rds")
+
+T15_4_gfblup_variances_all_1_1000=readRDS(file="T15_4_gfblup_variances_all_1_1000.rds")
+T15_4_gfblup_variances_all_1001_2000=readRDS(file="T15_4_gfblup_variances_all_1001_2000.rds")
+T15_4_gfblup_variances_all_2001_3000=readRDS(file="T15_4_gfblup_variances_all_2001_3000.rds")
+T15_4_gfblup_variances_all_3001_4000=readRDS(file="T15_4_gfblup_variances_all_3001_4000.rds")
+T15_4_gfblup_variances_all_4001_5000=readRDS(file="T15_4_gfblup_variances_all_4001_5000.rds")
+T15_4_gfblup_variances_all_5001_6000=readRDS(file="T15_4_gfblup_variances_all_5001_6000.rds")
+T15_4_gfblup_variances_all_6001_7000=readRDS(file="T15_4_gfblup_variances_all_6001_7000.rds")
+T15_4_gfblup_variances_all_7001_8000=readRDS(file="T15_4_gfblup_variances_all_7001_8000.rds")
+T15_4_gfblup_variances_all_8001_9000=readRDS(file="T15_4_gfblup_variances_all_8001_9000.rds")
+T15_4_gfblup_variances_all_9001_10000=readRDS(file="T15_4_gfblup_variances_all_9001_10000.rds")
+T15_4_gfblup_variances_all_10001_11000=readRDS(file="T15_4_gfblup_variances_all_10001_11000.rds")
+T15_4_gfblup_variances_all_11001_12419=readRDS(file="T15_4_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T15_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_4_gfblup_variances_all=rep(list(list()),cycles)
+T15_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_1_1000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_1001_2000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_2001_3000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_3001_4000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_4001_5000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_5001_6000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_6001_7000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_7001_8000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_8001_9000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_9001_10000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_10001_11000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_11001_12419[[r]])
+
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_1_1000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_1001_2000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_2001_3000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_3001_4000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_4001_5000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_5001_6000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_6001_7000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_7001_8000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_8001_9000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_9001_10000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_10001_11000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T15_4_gfblup_prediction_all,"T15_4_gfblup_prediction_all.rds")
+saveRDS(T15_4_gfblup_variances_all,"T15_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_5_gblup_prediction_all_1_1000=readRDS(file="T15_5_gblup_prediction_all_1_1000.rds")
+T15_5_gblup_prediction_all_1001_2000=readRDS(file="T15_5_gblup_prediction_all_1001_2000.rds")
+T15_5_gblup_prediction_all_2001_3000=readRDS(file="T15_5_gblup_prediction_all_2001_3000.rds")
+T15_5_gblup_prediction_all_3001_4000=readRDS(file="T15_5_gblup_prediction_all_3001_4000.rds")
+T15_5_gblup_prediction_all_4001_5000=readRDS(file="T15_5_gblup_prediction_all_4001_5000.rds")
+T15_5_gblup_prediction_all_5001_6000=readRDS(file="T15_5_gblup_prediction_all_5001_6000.rds")
+T15_5_gblup_prediction_all_6001_7000=readRDS(file="T15_5_gblup_prediction_all_6001_7000.rds")
+T15_5_gblup_prediction_all_7001_8000=readRDS(file="T15_5_gblup_prediction_all_7001_8000.rds")
+T15_5_gblup_prediction_all_8001_9000=readRDS(file="T15_5_gblup_prediction_all_8001_9000.rds")
+T15_5_gblup_prediction_all_9001_10000=readRDS(file="T15_5_gblup_prediction_all_9001_10000.rds")
+T15_5_gblup_prediction_all_10001_11000=readRDS(file="T15_5_gblup_prediction_all_10001_11000.rds")
+T15_5_gblup_prediction_all_11001_12419=readRDS(file="T15_5_gblup_prediction_all_11001_12419.rds")
+T15_5_gblup_prediction_all=c(T15_5_gblup_prediction_all_1_1000,T15_5_gblup_prediction_all_1001_2000,T15_5_gblup_prediction_all_2001_3000,T15_5_gblup_prediction_all_3001_4000,T15_5_gblup_prediction_all_4001_5000,T15_5_gblup_prediction_all_5001_6000,T15_5_gblup_prediction_all_6001_7000,T15_5_gblup_prediction_all_7001_8000,T15_5_gblup_prediction_all_8001_9000,T15_5_gblup_prediction_all_9001_10000,T15_5_gblup_prediction_all_10001_11000,T15_5_gblup_prediction_all_11001_12419)
+
+T15_5_gblup_variances_all_1_1000=readRDS(file="T15_5_gblup_variances_all_1_1000.rds")
+T15_5_gblup_variances_all_1001_2000=readRDS(file="T15_5_gblup_variances_all_1001_2000.rds")
+T15_5_gblup_variances_all_2001_3000=readRDS(file="T15_5_gblup_variances_all_2001_3000.rds")
+T15_5_gblup_variances_all_3001_4000=readRDS(file="T15_5_gblup_variances_all_3001_4000.rds")
+T15_5_gblup_variances_all_4001_5000=readRDS(file="T15_5_gblup_variances_all_4001_5000.rds")
+T15_5_gblup_variances_all_5001_6000=readRDS(file="T15_5_gblup_variances_all_5001_6000.rds")
+T15_5_gblup_variances_all_6001_7000=readRDS(file="T15_5_gblup_variances_all_6001_7000.rds")
+T15_5_gblup_variances_all_7001_8000=readRDS(file="T15_5_gblup_variances_all_7001_8000.rds")
+T15_5_gblup_variances_all_8001_9000=readRDS(file="T15_5_gblup_variances_all_8001_9000.rds")
+T15_5_gblup_variances_all_9001_10000=readRDS(file="T15_5_gblup_variances_all_9001_10000.rds")
+T15_5_gblup_variances_all_10001_11000=readRDS(file="T15_5_gblup_variances_all_10001_11000.rds")
+T15_5_gblup_variances_all_11001_12419=readRDS(file="T15_5_gblup_variances_all_11001_12419.rds")
+T15_5_gblup_variances_all=c(T15_5_gblup_variances_all_1_1000,T15_5_gblup_variances_all_1001_2000,T15_5_gblup_variances_all_2001_3000,T15_5_gblup_variances_all_3001_4000,T15_5_gblup_variances_all_4001_5000,T15_5_gblup_variances_all_5001_6000,T15_5_gblup_variances_all_6001_7000,T15_5_gblup_variances_all_7001_8000,T15_5_gblup_variances_all_8001_9000,T15_5_gblup_variances_all_9001_10000,T15_5_gblup_variances_all_10001_11000,T15_5_gblup_variances_all_11001_12419)
+
+saveRDS(T15_5_gblup_prediction_all,"T15_5_gblup_prediction_all.rds")
+saveRDS(T15_5_gblup_variances_all,"T15_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_5_gfblup_prediction_all_1_1000=readRDS(file="T15_5_gfblup_prediction_all_1_1000.rds")
+T15_5_gfblup_prediction_all_1001_2000=readRDS(file="T15_5_gfblup_prediction_all_1001_2000.rds")
+T15_5_gfblup_prediction_all_2001_3000=readRDS(file="T15_5_gfblup_prediction_all_2001_3000.rds")
+T15_5_gfblup_prediction_all_3001_4000=readRDS(file="T15_5_gfblup_prediction_all_3001_4000.rds")
+T15_5_gfblup_prediction_all_4001_5000=readRDS(file="T15_5_gfblup_prediction_all_4001_5000.rds")
+T15_5_gfblup_prediction_all_5001_6000=readRDS(file="T15_5_gfblup_prediction_all_5001_6000.rds")
+T15_5_gfblup_prediction_all_6001_7000=readRDS(file="T15_5_gfblup_prediction_all_6001_7000.rds")
+T15_5_gfblup_prediction_all_7001_8000=readRDS(file="T15_5_gfblup_prediction_all_7001_8000.rds")
+T15_5_gfblup_prediction_all_8001_9000=readRDS(file="T15_5_gfblup_prediction_all_8001_9000.rds")
+T15_5_gfblup_prediction_all_9001_10000=readRDS(file="T15_5_gfblup_prediction_all_9001_10000.rds")
+T15_5_gfblup_prediction_all_10001_11000=readRDS(file="T15_5_gfblup_prediction_all_10001_11000.rds")
+T15_5_gfblup_prediction_all_11001_12419=readRDS(file="T15_5_gfblup_prediction_all_11001_12419.rds")
+
+T15_5_gfblup_variances_all_1_1000=readRDS(file="T15_5_gfblup_variances_all_1_1000.rds")
+T15_5_gfblup_variances_all_1001_2000=readRDS(file="T15_5_gfblup_variances_all_1001_2000.rds")
+T15_5_gfblup_variances_all_2001_3000=readRDS(file="T15_5_gfblup_variances_all_2001_3000.rds")
+T15_5_gfblup_variances_all_3001_4000=readRDS(file="T15_5_gfblup_variances_all_3001_4000.rds")
+T15_5_gfblup_variances_all_4001_5000=readRDS(file="T15_5_gfblup_variances_all_4001_5000.rds")
+T15_5_gfblup_variances_all_5001_6000=readRDS(file="T15_5_gfblup_variances_all_5001_6000.rds")
+T15_5_gfblup_variances_all_6001_7000=readRDS(file="T15_5_gfblup_variances_all_6001_7000.rds")
+T15_5_gfblup_variances_all_7001_8000=readRDS(file="T15_5_gfblup_variances_all_7001_8000.rds")
+T15_5_gfblup_variances_all_8001_9000=readRDS(file="T15_5_gfblup_variances_all_8001_9000.rds")
+T15_5_gfblup_variances_all_9001_10000=readRDS(file="T15_5_gfblup_variances_all_9001_10000.rds")
+T15_5_gfblup_variances_all_10001_11000=readRDS(file="T15_5_gfblup_variances_all_10001_11000.rds")
+T15_5_gfblup_variances_all_11001_12419=readRDS(file="T15_5_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T15_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_5_gfblup_variances_all=rep(list(list()),cycles)
+T15_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_1_1000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_1001_2000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_2001_3000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_3001_4000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_4001_5000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_5001_6000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_6001_7000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_7001_8000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_8001_9000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_9001_10000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_10001_11000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_11001_12419[[r]])
+
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_1_1000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_1001_2000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_2001_3000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_3001_4000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_4001_5000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_5001_6000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_6001_7000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_7001_8000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_8001_9000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_9001_10000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_10001_11000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T15_5_gfblup_prediction_all,"T15_5_gfblup_prediction_all.rds")
+saveRDS(T15_5_gfblup_variances_all,"T15_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_6_gblup_prediction_all_1_1000=readRDS(file="T15_6_gblup_prediction_all_1_1000.rds")
+T15_6_gblup_prediction_all_1001_2000=readRDS(file="T15_6_gblup_prediction_all_1001_2000.rds")
+T15_6_gblup_prediction_all_2001_3000=readRDS(file="T15_6_gblup_prediction_all_2001_3000.rds")
+T15_6_gblup_prediction_all_3001_4000=readRDS(file="T15_6_gblup_prediction_all_3001_4000.rds")
+T15_6_gblup_prediction_all_4001_5000=readRDS(file="T15_6_gblup_prediction_all_4001_5000.rds")
+T15_6_gblup_prediction_all_5001_6000=readRDS(file="T15_6_gblup_prediction_all_5001_6000.rds")
+T15_6_gblup_prediction_all_6001_7000=readRDS(file="T15_6_gblup_prediction_all_6001_7000.rds")
+T15_6_gblup_prediction_all_7001_8000=readRDS(file="T15_6_gblup_prediction_all_7001_8000.rds")
+T15_6_gblup_prediction_all_8001_9000=readRDS(file="T15_6_gblup_prediction_all_8001_9000.rds")
+T15_6_gblup_prediction_all_9001_10000=readRDS(file="T15_6_gblup_prediction_all_9001_10000.rds")
+T15_6_gblup_prediction_all_10001_11000=readRDS(file="T15_6_gblup_prediction_all_10001_11000.rds")
+T15_6_gblup_prediction_all_11001_12419=readRDS(file="T15_6_gblup_prediction_all_11001_12419.rds")
+T15_6_gblup_prediction_all=c(T15_6_gblup_prediction_all_1_1000,T15_6_gblup_prediction_all_1001_2000,T15_6_gblup_prediction_all_2001_3000,T15_6_gblup_prediction_all_3001_4000,T15_6_gblup_prediction_all_4001_5000,T15_6_gblup_prediction_all_5001_6000,T15_6_gblup_prediction_all_6001_7000,T15_6_gblup_prediction_all_7001_8000,T15_6_gblup_prediction_all_8001_9000,T15_6_gblup_prediction_all_9001_10000,T15_6_gblup_prediction_all_10001_11000,T15_6_gblup_prediction_all_11001_12419)
+
+T15_6_gblup_variances_all_1_1000=readRDS(file="T15_6_gblup_variances_all_1_1000.rds")
+T15_6_gblup_variances_all_1001_2000=readRDS(file="T15_6_gblup_variances_all_1001_2000.rds")
+T15_6_gblup_variances_all_2001_3000=readRDS(file="T15_6_gblup_variances_all_2001_3000.rds")
+T15_6_gblup_variances_all_3001_4000=readRDS(file="T15_6_gblup_variances_all_3001_4000.rds")
+T15_6_gblup_variances_all_4001_5000=readRDS(file="T15_6_gblup_variances_all_4001_5000.rds")
+T15_6_gblup_variances_all_5001_6000=readRDS(file="T15_6_gblup_variances_all_5001_6000.rds")
+T15_6_gblup_variances_all_6001_7000=readRDS(file="T15_6_gblup_variances_all_6001_7000.rds")
+T15_6_gblup_variances_all_7001_8000=readRDS(file="T15_6_gblup_variances_all_7001_8000.rds")
+T15_6_gblup_variances_all_8001_9000=readRDS(file="T15_6_gblup_variances_all_8001_9000.rds")
+T15_6_gblup_variances_all_9001_10000=readRDS(file="T15_6_gblup_variances_all_9001_10000.rds")
+T15_6_gblup_variances_all_10001_11000=readRDS(file="T15_6_gblup_variances_all_10001_11000.rds")
+T15_6_gblup_variances_all_11001_12419=readRDS(file="T15_6_gblup_variances_all_11001_12419.rds")
+T15_6_gblup_variances_all=c(T15_6_gblup_variances_all_1_1000,T15_6_gblup_variances_all_1001_2000,T15_6_gblup_variances_all_2001_3000,T15_6_gblup_variances_all_3001_4000,T15_6_gblup_variances_all_4001_5000,T15_6_gblup_variances_all_5001_6000,T15_6_gblup_variances_all_6001_7000,T15_6_gblup_variances_all_7001_8000,T15_6_gblup_variances_all_8001_9000,T15_6_gblup_variances_all_9001_10000,T15_6_gblup_variances_all_10001_11000,T15_6_gblup_variances_all_11001_12419)
+
+saveRDS(T15_6_gblup_prediction_all,"T15_6_gblup_prediction_all.rds")
+saveRDS(T15_6_gblup_variances_all,"T15_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_6_gfblup_prediction_all_1_1000=readRDS(file="T15_6_gfblup_prediction_all_1_1000.rds")
+T15_6_gfblup_prediction_all_1001_2000=readRDS(file="T15_6_gfblup_prediction_all_1001_2000.rds")
+T15_6_gfblup_prediction_all_2001_3000=readRDS(file="T15_6_gfblup_prediction_all_2001_3000.rds")
+T15_6_gfblup_prediction_all_3001_4000=readRDS(file="T15_6_gfblup_prediction_all_3001_4000.rds")
+T15_6_gfblup_prediction_all_4001_5000=readRDS(file="T15_6_gfblup_prediction_all_4001_5000.rds")
+T15_6_gfblup_prediction_all_5001_6000=readRDS(file="T15_6_gfblup_prediction_all_5001_6000.rds")
+T15_6_gfblup_prediction_all_6001_7000=readRDS(file="T15_6_gfblup_prediction_all_6001_7000.rds")
+T15_6_gfblup_prediction_all_7001_8000=readRDS(file="T15_6_gfblup_prediction_all_7001_8000.rds")
+T15_6_gfblup_prediction_all_8001_9000=readRDS(file="T15_6_gfblup_prediction_all_8001_9000.rds")
+T15_6_gfblup_prediction_all_9001_10000=readRDS(file="T15_6_gfblup_prediction_all_9001_10000.rds")
+T15_6_gfblup_prediction_all_10001_11000=readRDS(file="T15_6_gfblup_prediction_all_10001_11000.rds")
+T15_6_gfblup_prediction_all_11001_12419=readRDS(file="T15_6_gfblup_prediction_all_11001_12419.rds")
+
+T15_6_gfblup_variances_all_1_1000=readRDS(file="T15_6_gfblup_variances_all_1_1000.rds")
+T15_6_gfblup_variances_all_1001_2000=readRDS(file="T15_6_gfblup_variances_all_1001_2000.rds")
+T15_6_gfblup_variances_all_2001_3000=readRDS(file="T15_6_gfblup_variances_all_2001_3000.rds")
+T15_6_gfblup_variances_all_3001_4000=readRDS(file="T15_6_gfblup_variances_all_3001_4000.rds")
+T15_6_gfblup_variances_all_4001_5000=readRDS(file="T15_6_gfblup_variances_all_4001_5000.rds")
+T15_6_gfblup_variances_all_5001_6000=readRDS(file="T15_6_gfblup_variances_all_5001_6000.rds")
+T15_6_gfblup_variances_all_6001_7000=readRDS(file="T15_6_gfblup_variances_all_6001_7000.rds")
+T15_6_gfblup_variances_all_7001_8000=readRDS(file="T15_6_gfblup_variances_all_7001_8000.rds")
+T15_6_gfblup_variances_all_8001_9000=readRDS(file="T15_6_gfblup_variances_all_8001_9000.rds")
+T15_6_gfblup_variances_all_9001_10000=readRDS(file="T15_6_gfblup_variances_all_9001_10000.rds")
+T15_6_gfblup_variances_all_10001_11000=readRDS(file="T15_6_gfblup_variances_all_10001_11000.rds")
+T15_6_gfblup_variances_all_11001_12419=readRDS(file="T15_6_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T15_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_6_gfblup_variances_all=rep(list(list()),cycles)
+T15_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_1_1000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_1001_2000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_2001_3000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_3001_4000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_4001_5000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_5001_6000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_6001_7000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_7001_8000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_8001_9000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_9001_10000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_10001_11000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_11001_12419[[r]])
+
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_1_1000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_1001_2000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_2001_3000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_3001_4000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_4001_5000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_5001_6000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_6001_7000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_7001_8000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_8001_9000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_9001_10000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_10001_11000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T15_6_gfblup_prediction_all,"T15_6_gfblup_prediction_all.rds")
+saveRDS(T15_6_gfblup_variances_all,"T15_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_7_gblup_prediction_all_1_1000=readRDS(file="T15_7_gblup_prediction_all_1_1000.rds")
+T15_7_gblup_prediction_all_1001_2000=readRDS(file="T15_7_gblup_prediction_all_1001_2000.rds")
+T15_7_gblup_prediction_all_2001_3000=readRDS(file="T15_7_gblup_prediction_all_2001_3000.rds")
+T15_7_gblup_prediction_all_3001_4000=readRDS(file="T15_7_gblup_prediction_all_3001_4000.rds")
+T15_7_gblup_prediction_all_4001_5000=readRDS(file="T15_7_gblup_prediction_all_4001_5000.rds")
+T15_7_gblup_prediction_all_5001_6000=readRDS(file="T15_7_gblup_prediction_all_5001_6000.rds")
+T15_7_gblup_prediction_all_6001_7000=readRDS(file="T15_7_gblup_prediction_all_6001_7000.rds")
+T15_7_gblup_prediction_all_7001_8000=readRDS(file="T15_7_gblup_prediction_all_7001_8000.rds")
+T15_7_gblup_prediction_all_8001_9000=readRDS(file="T15_7_gblup_prediction_all_8001_9000.rds")
+T15_7_gblup_prediction_all_9001_10000=readRDS(file="T15_7_gblup_prediction_all_9001_10000.rds")
+T15_7_gblup_prediction_all_10001_11000=readRDS(file="T15_7_gblup_prediction_all_10001_11000.rds")
+T15_7_gblup_prediction_all_11001_12419=readRDS(file="T15_7_gblup_prediction_all_11001_12419.rds")
+T15_7_gblup_prediction_all=c(T15_7_gblup_prediction_all_1_1000,T15_7_gblup_prediction_all_1001_2000,T15_7_gblup_prediction_all_2001_3000,T15_7_gblup_prediction_all_3001_4000,T15_7_gblup_prediction_all_4001_5000,T15_7_gblup_prediction_all_5001_6000,T15_7_gblup_prediction_all_6001_7000,T15_7_gblup_prediction_all_7001_8000,T15_7_gblup_prediction_all_8001_9000,T15_7_gblup_prediction_all_9001_10000,T15_7_gblup_prediction_all_10001_11000,T15_7_gblup_prediction_all_11001_12419)
+
+T15_7_gblup_variances_all_1_1000=readRDS(file="T15_7_gblup_variances_all_1_1000.rds")
+T15_7_gblup_variances_all_1001_2000=readRDS(file="T15_7_gblup_variances_all_1001_2000.rds")
+T15_7_gblup_variances_all_2001_3000=readRDS(file="T15_7_gblup_variances_all_2001_3000.rds")
+T15_7_gblup_variances_all_3001_4000=readRDS(file="T15_7_gblup_variances_all_3001_4000.rds")
+T15_7_gblup_variances_all_4001_5000=readRDS(file="T15_7_gblup_variances_all_4001_5000.rds")
+T15_7_gblup_variances_all_5001_6000=readRDS(file="T15_7_gblup_variances_all_5001_6000.rds")
+T15_7_gblup_variances_all_6001_7000=readRDS(file="T15_7_gblup_variances_all_6001_7000.rds")
+T15_7_gblup_variances_all_7001_8000=readRDS(file="T15_7_gblup_variances_all_7001_8000.rds")
+T15_7_gblup_variances_all_8001_9000=readRDS(file="T15_7_gblup_variances_all_8001_9000.rds")
+T15_7_gblup_variances_all_9001_10000=readRDS(file="T15_7_gblup_variances_all_9001_10000.rds")
+T15_7_gblup_variances_all_10001_11000=readRDS(file="T15_7_gblup_variances_all_10001_11000.rds")
+T15_7_gblup_variances_all_11001_12419=readRDS(file="T15_7_gblup_variances_all_11001_12419.rds")
+T15_7_gblup_variances_all=c(T15_7_gblup_variances_all_1_1000,T15_7_gblup_variances_all_1001_2000,T15_7_gblup_variances_all_2001_3000,T15_7_gblup_variances_all_3001_4000,T15_7_gblup_variances_all_4001_5000,T15_7_gblup_variances_all_5001_6000,T15_7_gblup_variances_all_6001_7000,T15_7_gblup_variances_all_7001_8000,T15_7_gblup_variances_all_8001_9000,T15_7_gblup_variances_all_9001_10000,T15_7_gblup_variances_all_10001_11000,T15_7_gblup_variances_all_11001_12419)
+
+saveRDS(T15_7_gblup_prediction_all,"T15_7_gblup_prediction_all.rds")
+saveRDS(T15_7_gblup_variances_all,"T15_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_7_gfblup_prediction_all_1_1000=readRDS(file="T15_7_gfblup_prediction_all_1_1000.rds")
+T15_7_gfblup_prediction_all_1001_2000=readRDS(file="T15_7_gfblup_prediction_all_1001_2000.rds")
+T15_7_gfblup_prediction_all_2001_3000=readRDS(file="T15_7_gfblup_prediction_all_2001_3000.rds")
+T15_7_gfblup_prediction_all_3001_4000=readRDS(file="T15_7_gfblup_prediction_all_3001_4000.rds")
+T15_7_gfblup_prediction_all_4001_5000=readRDS(file="T15_7_gfblup_prediction_all_4001_5000.rds")
+T15_7_gfblup_prediction_all_5001_6000=readRDS(file="T15_7_gfblup_prediction_all_5001_6000.rds")
+T15_7_gfblup_prediction_all_6001_7000=readRDS(file="T15_7_gfblup_prediction_all_6001_7000.rds")
+T15_7_gfblup_prediction_all_7001_8000=readRDS(file="T15_7_gfblup_prediction_all_7001_8000.rds")
+T15_7_gfblup_prediction_all_8001_9000=readRDS(file="T15_7_gfblup_prediction_all_8001_9000.rds")
+T15_7_gfblup_prediction_all_9001_10000=readRDS(file="T15_7_gfblup_prediction_all_9001_10000.rds")
+T15_7_gfblup_prediction_all_10001_11000=readRDS(file="T15_7_gfblup_prediction_all_10001_11000.rds")
+T15_7_gfblup_prediction_all_11001_12419=readRDS(file="T15_7_gfblup_prediction_all_11001_12419.rds")
+
+T15_7_gfblup_variances_all_1_1000=readRDS(file="T15_7_gfblup_variances_all_1_1000.rds")
+T15_7_gfblup_variances_all_1001_2000=readRDS(file="T15_7_gfblup_variances_all_1001_2000.rds")
+T15_7_gfblup_variances_all_2001_3000=readRDS(file="T15_7_gfblup_variances_all_2001_3000.rds")
+T15_7_gfblup_variances_all_3001_4000=readRDS(file="T15_7_gfblup_variances_all_3001_4000.rds")
+T15_7_gfblup_variances_all_4001_5000=readRDS(file="T15_7_gfblup_variances_all_4001_5000.rds")
+T15_7_gfblup_variances_all_5001_6000=readRDS(file="T15_7_gfblup_variances_all_5001_6000.rds")
+T15_7_gfblup_variances_all_6001_7000=readRDS(file="T15_7_gfblup_variances_all_6001_7000.rds")
+T15_7_gfblup_variances_all_7001_8000=readRDS(file="T15_7_gfblup_variances_all_7001_8000.rds")
+T15_7_gfblup_variances_all_8001_9000=readRDS(file="T15_7_gfblup_variances_all_8001_9000.rds")
+T15_7_gfblup_variances_all_9001_10000=readRDS(file="T15_7_gfblup_variances_all_9001_10000.rds")
+T15_7_gfblup_variances_all_10001_11000=readRDS(file="T15_7_gfblup_variances_all_10001_11000.rds")
+T15_7_gfblup_variances_all_11001_12419=readRDS(file="T15_7_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T15_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_7_gfblup_variances_all=rep(list(list()),cycles)
+T15_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_1_1000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_1001_2000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_2001_3000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_3001_4000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_4001_5000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_5001_6000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_6001_7000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_7001_8000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_8001_9000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_9001_10000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_10001_11000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_11001_12419[[r]])
+
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_1_1000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_1001_2000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_2001_3000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_3001_4000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_4001_5000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_5001_6000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_6001_7000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_7001_8000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_8001_9000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_9001_10000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_10001_11000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T15_7_gfblup_prediction_all,"T15_7_gfblup_prediction_all.rds")
+saveRDS(T15_7_gfblup_variances_all,"T15_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_8_gblup_prediction_all_1_1000=readRDS(file="T15_8_gblup_prediction_all_1_1000.rds")
+T15_8_gblup_prediction_all_1001_2000=readRDS(file="T15_8_gblup_prediction_all_1001_2000.rds")
+T15_8_gblup_prediction_all_2001_3000=readRDS(file="T15_8_gblup_prediction_all_2001_3000.rds")
+T15_8_gblup_prediction_all_3001_4000=readRDS(file="T15_8_gblup_prediction_all_3001_4000.rds")
+T15_8_gblup_prediction_all_4001_5000=readRDS(file="T15_8_gblup_prediction_all_4001_5000.rds")
+T15_8_gblup_prediction_all_5001_6000=readRDS(file="T15_8_gblup_prediction_all_5001_6000.rds")
+T15_8_gblup_prediction_all_6001_7000=readRDS(file="T15_8_gblup_prediction_all_6001_7000.rds")
+T15_8_gblup_prediction_all_7001_8000=readRDS(file="T15_8_gblup_prediction_all_7001_8000.rds")
+T15_8_gblup_prediction_all_8001_9000=readRDS(file="T15_8_gblup_prediction_all_8001_9000.rds")
+T15_8_gblup_prediction_all_9001_10000=readRDS(file="T15_8_gblup_prediction_all_9001_10000.rds")
+T15_8_gblup_prediction_all_10001_11000=readRDS(file="T15_8_gblup_prediction_all_10001_11000.rds")
+T15_8_gblup_prediction_all_11001_12419=readRDS(file="T15_8_gblup_prediction_all_11001_12419.rds")
+T15_8_gblup_prediction_all=c(T15_8_gblup_prediction_all_1_1000,T15_8_gblup_prediction_all_1001_2000,T15_8_gblup_prediction_all_2001_3000,T15_8_gblup_prediction_all_3001_4000,T15_8_gblup_prediction_all_4001_5000,T15_8_gblup_prediction_all_5001_6000,T15_8_gblup_prediction_all_6001_7000,T15_8_gblup_prediction_all_7001_8000,T15_8_gblup_prediction_all_8001_9000,T15_8_gblup_prediction_all_9001_10000,T15_8_gblup_prediction_all_10001_11000,T15_8_gblup_prediction_all_11001_12419)
+
+T15_8_gblup_variances_all_1_1000=readRDS(file="T15_8_gblup_variances_all_1_1000.rds")
+T15_8_gblup_variances_all_1001_2000=readRDS(file="T15_8_gblup_variances_all_1001_2000.rds")
+T15_8_gblup_variances_all_2001_3000=readRDS(file="T15_8_gblup_variances_all_2001_3000.rds")
+T15_8_gblup_variances_all_3001_4000=readRDS(file="T15_8_gblup_variances_all_3001_4000.rds")
+T15_8_gblup_variances_all_4001_5000=readRDS(file="T15_8_gblup_variances_all_4001_5000.rds")
+T15_8_gblup_variances_all_5001_6000=readRDS(file="T15_8_gblup_variances_all_5001_6000.rds")
+T15_8_gblup_variances_all_6001_7000=readRDS(file="T15_8_gblup_variances_all_6001_7000.rds")
+T15_8_gblup_variances_all_7001_8000=readRDS(file="T15_8_gblup_variances_all_7001_8000.rds")
+T15_8_gblup_variances_all_8001_9000=readRDS(file="T15_8_gblup_variances_all_8001_9000.rds")
+T15_8_gblup_variances_all_9001_10000=readRDS(file="T15_8_gblup_variances_all_9001_10000.rds")
+T15_8_gblup_variances_all_10001_11000=readRDS(file="T15_8_gblup_variances_all_10001_11000.rds")
+T15_8_gblup_variances_all_11001_12419=readRDS(file="T15_8_gblup_variances_all_11001_12419.rds")
+T15_8_gblup_variances_all=c(T15_8_gblup_variances_all_1_1000,T15_8_gblup_variances_all_1001_2000,T15_8_gblup_variances_all_2001_3000,T15_8_gblup_variances_all_3001_4000,T15_8_gblup_variances_all_4001_5000,T15_8_gblup_variances_all_5001_6000,T15_8_gblup_variances_all_6001_7000,T15_8_gblup_variances_all_7001_8000,T15_8_gblup_variances_all_8001_9000,T15_8_gblup_variances_all_9001_10000,T15_8_gblup_variances_all_10001_11000,T15_8_gblup_variances_all_11001_12419)
+
+saveRDS(T15_8_gblup_prediction_all,"T15_8_gblup_prediction_all.rds")
+saveRDS(T15_8_gblup_variances_all,"T15_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_8_gfblup_prediction_all_1_1000=readRDS(file="T15_8_gfblup_prediction_all_1_1000.rds")
+T15_8_gfblup_prediction_all_1001_2000=readRDS(file="T15_8_gfblup_prediction_all_1001_2000.rds")
+T15_8_gfblup_prediction_all_2001_3000=readRDS(file="T15_8_gfblup_prediction_all_2001_3000.rds")
+T15_8_gfblup_prediction_all_3001_4000=readRDS(file="T15_8_gfblup_prediction_all_3001_4000.rds")
+T15_8_gfblup_prediction_all_4001_5000=readRDS(file="T15_8_gfblup_prediction_all_4001_5000.rds")
+T15_8_gfblup_prediction_all_5001_6000=readRDS(file="T15_8_gfblup_prediction_all_5001_6000.rds")
+T15_8_gfblup_prediction_all_6001_7000=readRDS(file="T15_8_gfblup_prediction_all_6001_7000.rds")
+T15_8_gfblup_prediction_all_7001_8000=readRDS(file="T15_8_gfblup_prediction_all_7001_8000.rds")
+T15_8_gfblup_prediction_all_8001_9000=readRDS(file="T15_8_gfblup_prediction_all_8001_9000.rds")
+T15_8_gfblup_prediction_all_9001_10000=readRDS(file="T15_8_gfblup_prediction_all_9001_10000.rds")
+T15_8_gfblup_prediction_all_10001_11000=readRDS(file="T15_8_gfblup_prediction_all_10001_11000.rds")
+T15_8_gfblup_prediction_all_11001_12419=readRDS(file="T15_8_gfblup_prediction_all_11001_12419.rds")
+
+T15_8_gfblup_variances_all_1_1000=readRDS(file="T15_8_gfblup_variances_all_1_1000.rds")
+T15_8_gfblup_variances_all_1001_2000=readRDS(file="T15_8_gfblup_variances_all_1001_2000.rds")
+T15_8_gfblup_variances_all_2001_3000=readRDS(file="T15_8_gfblup_variances_all_2001_3000.rds")
+T15_8_gfblup_variances_all_3001_4000=readRDS(file="T15_8_gfblup_variances_all_3001_4000.rds")
+T15_8_gfblup_variances_all_4001_5000=readRDS(file="T15_8_gfblup_variances_all_4001_5000.rds")
+T15_8_gfblup_variances_all_5001_6000=readRDS(file="T15_8_gfblup_variances_all_5001_6000.rds")
+T15_8_gfblup_variances_all_6001_7000=readRDS(file="T15_8_gfblup_variances_all_6001_7000.rds")
+T15_8_gfblup_variances_all_7001_8000=readRDS(file="T15_8_gfblup_variances_all_7001_8000.rds")
+T15_8_gfblup_variances_all_8001_9000=readRDS(file="T15_8_gfblup_variances_all_8001_9000.rds")
+T15_8_gfblup_variances_all_9001_10000=readRDS(file="T15_8_gfblup_variances_all_9001_10000.rds")
+T15_8_gfblup_variances_all_10001_11000=readRDS(file="T15_8_gfblup_variances_all_10001_11000.rds")
+T15_8_gfblup_variances_all_11001_12419=readRDS(file="T15_8_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T15_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_8_gfblup_variances_all=rep(list(list()),cycles)
+T15_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_1_1000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_1001_2000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_2001_3000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_3001_4000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_4001_5000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_5001_6000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_6001_7000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_7001_8000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_8001_9000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_9001_10000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_10001_11000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_11001_12419[[r]])
+
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_1_1000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_1001_2000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_2001_3000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_3001_4000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_4001_5000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_5001_6000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_6001_7000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_7001_8000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_8001_9000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_9001_10000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_10001_11000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T15_8_gfblup_prediction_all,"T15_8_gfblup_prediction_all.rds")
+saveRDS(T15_8_gfblup_variances_all,"T15_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_1_gblup_prediction_all_1_1000=readRDS(file="T16_1_gblup_prediction_all_1_1000.rds")
+T16_1_gblup_prediction_all_1001_2000=readRDS(file="T16_1_gblup_prediction_all_1001_2000.rds")
+T16_1_gblup_prediction_all_2001_3000=readRDS(file="T16_1_gblup_prediction_all_2001_3000.rds")
+T16_1_gblup_prediction_all_3001_4000=readRDS(file="T16_1_gblup_prediction_all_3001_4000.rds")
+T16_1_gblup_prediction_all_4001_5000=readRDS(file="T16_1_gblup_prediction_all_4001_5000.rds")
+T16_1_gblup_prediction_all_5001_6000=readRDS(file="T16_1_gblup_prediction_all_5001_6000.rds")
+T16_1_gblup_prediction_all_6001_7000=readRDS(file="T16_1_gblup_prediction_all_6001_7000.rds")
+T16_1_gblup_prediction_all_7001_8000=readRDS(file="T16_1_gblup_prediction_all_7001_8000.rds")
+T16_1_gblup_prediction_all_8001_9000=readRDS(file="T16_1_gblup_prediction_all_8001_9000.rds")
+T16_1_gblup_prediction_all_9001_10000=readRDS(file="T16_1_gblup_prediction_all_9001_10000.rds")
+T16_1_gblup_prediction_all_10001_11000=readRDS(file="T16_1_gblup_prediction_all_10001_11000.rds")
+T16_1_gblup_prediction_all_11001_12419=readRDS(file="T16_1_gblup_prediction_all_11001_12419.rds")
+T16_1_gblup_prediction_all=c(T16_1_gblup_prediction_all_1_1000,T16_1_gblup_prediction_all_1001_2000,T16_1_gblup_prediction_all_2001_3000,T16_1_gblup_prediction_all_3001_4000,T16_1_gblup_prediction_all_4001_5000,T16_1_gblup_prediction_all_5001_6000,T16_1_gblup_prediction_all_6001_7000,T16_1_gblup_prediction_all_7001_8000,T16_1_gblup_prediction_all_8001_9000,T16_1_gblup_prediction_all_9001_10000,T16_1_gblup_prediction_all_10001_11000,T16_1_gblup_prediction_all_11001_12419)
+
+T16_1_gblup_variances_all_1_1000=readRDS(file="T16_1_gblup_variances_all_1_1000.rds")
+T16_1_gblup_variances_all_1001_2000=readRDS(file="T16_1_gblup_variances_all_1001_2000.rds")
+T16_1_gblup_variances_all_2001_3000=readRDS(file="T16_1_gblup_variances_all_2001_3000.rds")
+T16_1_gblup_variances_all_3001_4000=readRDS(file="T16_1_gblup_variances_all_3001_4000.rds")
+T16_1_gblup_variances_all_4001_5000=readRDS(file="T16_1_gblup_variances_all_4001_5000.rds")
+T16_1_gblup_variances_all_5001_6000=readRDS(file="T16_1_gblup_variances_all_5001_6000.rds")
+T16_1_gblup_variances_all_6001_7000=readRDS(file="T16_1_gblup_variances_all_6001_7000.rds")
+T16_1_gblup_variances_all_7001_8000=readRDS(file="T16_1_gblup_variances_all_7001_8000.rds")
+T16_1_gblup_variances_all_8001_9000=readRDS(file="T16_1_gblup_variances_all_8001_9000.rds")
+T16_1_gblup_variances_all_9001_10000=readRDS(file="T16_1_gblup_variances_all_9001_10000.rds")
+T16_1_gblup_variances_all_10001_11000=readRDS(file="T16_1_gblup_variances_all_10001_11000.rds")
+T16_1_gblup_variances_all_11001_12419=readRDS(file="T16_1_gblup_variances_all_11001_12419.rds")
+T16_1_gblup_variances_all=c(T16_1_gblup_variances_all_1_1000,T16_1_gblup_variances_all_1001_2000,T16_1_gblup_variances_all_2001_3000,T16_1_gblup_variances_all_3001_4000,T16_1_gblup_variances_all_4001_5000,T16_1_gblup_variances_all_5001_6000,T16_1_gblup_variances_all_6001_7000,T16_1_gblup_variances_all_7001_8000,T16_1_gblup_variances_all_8001_9000,T16_1_gblup_variances_all_9001_10000,T16_1_gblup_variances_all_10001_11000,T16_1_gblup_variances_all_11001_12419)
+
+saveRDS(T16_1_gblup_prediction_all,"T16_1_gblup_prediction_all.rds")
+saveRDS(T16_1_gblup_variances_all,"T16_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_1_gfblup_prediction_all_1_1000=readRDS(file="T16_1_gfblup_prediction_all_1_1000.rds")
+T16_1_gfblup_prediction_all_1001_2000=readRDS(file="T16_1_gfblup_prediction_all_1001_2000.rds")
+T16_1_gfblup_prediction_all_2001_3000=readRDS(file="T16_1_gfblup_prediction_all_2001_3000.rds")
+T16_1_gfblup_prediction_all_3001_4000=readRDS(file="T16_1_gfblup_prediction_all_3001_4000.rds")
+T16_1_gfblup_prediction_all_4001_5000=readRDS(file="T16_1_gfblup_prediction_all_4001_5000.rds")
+T16_1_gfblup_prediction_all_5001_6000=readRDS(file="T16_1_gfblup_prediction_all_5001_6000.rds")
+T16_1_gfblup_prediction_all_6001_7000=readRDS(file="T16_1_gfblup_prediction_all_6001_7000.rds")
+T16_1_gfblup_prediction_all_7001_8000=readRDS(file="T16_1_gfblup_prediction_all_7001_8000.rds")
+T16_1_gfblup_prediction_all_8001_9000=readRDS(file="T16_1_gfblup_prediction_all_8001_9000.rds")
+T16_1_gfblup_prediction_all_9001_10000=readRDS(file="T16_1_gfblup_prediction_all_9001_10000.rds")
+T16_1_gfblup_prediction_all_10001_11000=readRDS(file="T16_1_gfblup_prediction_all_10001_11000.rds")
+T16_1_gfblup_prediction_all_11001_12419=readRDS(file="T16_1_gfblup_prediction_all_11001_12419.rds")
+
+T16_1_gfblup_variances_all_1_1000=readRDS(file="T16_1_gfblup_variances_all_1_1000.rds")
+T16_1_gfblup_variances_all_1001_2000=readRDS(file="T16_1_gfblup_variances_all_1001_2000.rds")
+T16_1_gfblup_variances_all_2001_3000=readRDS(file="T16_1_gfblup_variances_all_2001_3000.rds")
+T16_1_gfblup_variances_all_3001_4000=readRDS(file="T16_1_gfblup_variances_all_3001_4000.rds")
+T16_1_gfblup_variances_all_4001_5000=readRDS(file="T16_1_gfblup_variances_all_4001_5000.rds")
+T16_1_gfblup_variances_all_5001_6000=readRDS(file="T16_1_gfblup_variances_all_5001_6000.rds")
+T16_1_gfblup_variances_all_6001_7000=readRDS(file="T16_1_gfblup_variances_all_6001_7000.rds")
+T16_1_gfblup_variances_all_7001_8000=readRDS(file="T16_1_gfblup_variances_all_7001_8000.rds")
+T16_1_gfblup_variances_all_8001_9000=readRDS(file="T16_1_gfblup_variances_all_8001_9000.rds")
+T16_1_gfblup_variances_all_9001_10000=readRDS(file="T16_1_gfblup_variances_all_9001_10000.rds")
+T16_1_gfblup_variances_all_10001_11000=readRDS(file="T16_1_gfblup_variances_all_10001_11000.rds")
+T16_1_gfblup_variances_all_11001_12419=readRDS(file="T16_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T16_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_1_gfblup_variances_all=rep(list(list()),cycles)
+T16_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_1_1000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_1001_2000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_2001_3000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_3001_4000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_4001_5000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_5001_6000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_6001_7000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_7001_8000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_8001_9000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_9001_10000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_10001_11000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_11001_12419[[r]])
+
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_1_1000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_1001_2000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_2001_3000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_3001_4000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_4001_5000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_5001_6000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_6001_7000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_7001_8000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_8001_9000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_9001_10000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_10001_11000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T16_1_gfblup_prediction_all,"T16_1_gfblup_prediction_all.rds")
+saveRDS(T16_1_gfblup_variances_all,"T16_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_2_gblup_prediction_all_1_1000=readRDS(file="T16_2_gblup_prediction_all_1_1000.rds")
+T16_2_gblup_prediction_all_1001_2000=readRDS(file="T16_2_gblup_prediction_all_1001_2000.rds")
+T16_2_gblup_prediction_all_2001_3000=readRDS(file="T16_2_gblup_prediction_all_2001_3000.rds")
+T16_2_gblup_prediction_all_3001_4000=readRDS(file="T16_2_gblup_prediction_all_3001_4000.rds")
+T16_2_gblup_prediction_all_4001_5000=readRDS(file="T16_2_gblup_prediction_all_4001_5000.rds")
+T16_2_gblup_prediction_all_5001_6000=readRDS(file="T16_2_gblup_prediction_all_5001_6000.rds")
+T16_2_gblup_prediction_all_6001_7000=readRDS(file="T16_2_gblup_prediction_all_6001_7000.rds")
+T16_2_gblup_prediction_all_7001_8000=readRDS(file="T16_2_gblup_prediction_all_7001_8000.rds")
+T16_2_gblup_prediction_all_8001_9000=readRDS(file="T16_2_gblup_prediction_all_8001_9000.rds")
+T16_2_gblup_prediction_all_9001_10000=readRDS(file="T16_2_gblup_prediction_all_9001_10000.rds")
+T16_2_gblup_prediction_all_10001_11000=readRDS(file="T16_2_gblup_prediction_all_10001_11000.rds")
+T16_2_gblup_prediction_all_11001_12419=readRDS(file="T16_2_gblup_prediction_all_11001_12419.rds")
+T16_2_gblup_prediction_all=c(T16_2_gblup_prediction_all_1_1000,T16_2_gblup_prediction_all_1001_2000,T16_2_gblup_prediction_all_2001_3000,T16_2_gblup_prediction_all_3001_4000,T16_2_gblup_prediction_all_4001_5000,T16_2_gblup_prediction_all_5001_6000,T16_2_gblup_prediction_all_6001_7000,T16_2_gblup_prediction_all_7001_8000,T16_2_gblup_prediction_all_8001_9000,T16_2_gblup_prediction_all_9001_10000,T16_2_gblup_prediction_all_10001_11000,T16_2_gblup_prediction_all_11001_12419)
+
+T16_2_gblup_variances_all_1_1000=readRDS(file="T16_2_gblup_variances_all_1_1000.rds")
+T16_2_gblup_variances_all_1001_2000=readRDS(file="T16_2_gblup_variances_all_1001_2000.rds")
+T16_2_gblup_variances_all_2001_3000=readRDS(file="T16_2_gblup_variances_all_2001_3000.rds")
+T16_2_gblup_variances_all_3001_4000=readRDS(file="T16_2_gblup_variances_all_3001_4000.rds")
+T16_2_gblup_variances_all_4001_5000=readRDS(file="T16_2_gblup_variances_all_4001_5000.rds")
+T16_2_gblup_variances_all_5001_6000=readRDS(file="T16_2_gblup_variances_all_5001_6000.rds")
+T16_2_gblup_variances_all_6001_7000=readRDS(file="T16_2_gblup_variances_all_6001_7000.rds")
+T16_2_gblup_variances_all_7001_8000=readRDS(file="T16_2_gblup_variances_all_7001_8000.rds")
+T16_2_gblup_variances_all_8001_9000=readRDS(file="T16_2_gblup_variances_all_8001_9000.rds")
+T16_2_gblup_variances_all_9001_10000=readRDS(file="T16_2_gblup_variances_all_9001_10000.rds")
+T16_2_gblup_variances_all_10001_11000=readRDS(file="T16_2_gblup_variances_all_10001_11000.rds")
+T16_2_gblup_variances_all_11001_12419=readRDS(file="T16_2_gblup_variances_all_11001_12419.rds")
+T16_2_gblup_variances_all=c(T16_2_gblup_variances_all_1_1000,T16_2_gblup_variances_all_1001_2000,T16_2_gblup_variances_all_2001_3000,T16_2_gblup_variances_all_3001_4000,T16_2_gblup_variances_all_4001_5000,T16_2_gblup_variances_all_5001_6000,T16_2_gblup_variances_all_6001_7000,T16_2_gblup_variances_all_7001_8000,T16_2_gblup_variances_all_8001_9000,T16_2_gblup_variances_all_9001_10000,T16_2_gblup_variances_all_10001_11000,T16_2_gblup_variances_all_11001_12419)
+
+saveRDS(T16_2_gblup_prediction_all,"T16_2_gblup_prediction_all.rds")
+saveRDS(T16_2_gblup_variances_all,"T16_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_2_gfblup_prediction_all_1_1000=readRDS(file="T16_2_gfblup_prediction_all_1_1000.rds")
+T16_2_gfblup_prediction_all_1001_2000=readRDS(file="T16_2_gfblup_prediction_all_1001_2000.rds")
+T16_2_gfblup_prediction_all_2001_3000=readRDS(file="T16_2_gfblup_prediction_all_2001_3000.rds")
+T16_2_gfblup_prediction_all_3001_4000=readRDS(file="T16_2_gfblup_prediction_all_3001_4000.rds")
+T16_2_gfblup_prediction_all_4001_5000=readRDS(file="T16_2_gfblup_prediction_all_4001_5000.rds")
+T16_2_gfblup_prediction_all_5001_6000=readRDS(file="T16_2_gfblup_prediction_all_5001_6000.rds")
+T16_2_gfblup_prediction_all_6001_7000=readRDS(file="T16_2_gfblup_prediction_all_6001_7000.rds")
+T16_2_gfblup_prediction_all_7001_8000=readRDS(file="T16_2_gfblup_prediction_all_7001_8000.rds")
+T16_2_gfblup_prediction_all_8001_9000=readRDS(file="T16_2_gfblup_prediction_all_8001_9000.rds")
+T16_2_gfblup_prediction_all_9001_10000=readRDS(file="T16_2_gfblup_prediction_all_9001_10000.rds")
+T16_2_gfblup_prediction_all_10001_11000=readRDS(file="T16_2_gfblup_prediction_all_10001_11000.rds")
+T16_2_gfblup_prediction_all_11001_12419=readRDS(file="T16_2_gfblup_prediction_all_11001_12419.rds")
+
+T16_2_gfblup_variances_all_1_1000=readRDS(file="T16_2_gfblup_variances_all_1_1000.rds")
+T16_2_gfblup_variances_all_1001_2000=readRDS(file="T16_2_gfblup_variances_all_1001_2000.rds")
+T16_2_gfblup_variances_all_2001_3000=readRDS(file="T16_2_gfblup_variances_all_2001_3000.rds")
+T16_2_gfblup_variances_all_3001_4000=readRDS(file="T16_2_gfblup_variances_all_3001_4000.rds")
+T16_2_gfblup_variances_all_4001_5000=readRDS(file="T16_2_gfblup_variances_all_4001_5000.rds")
+T16_2_gfblup_variances_all_5001_6000=readRDS(file="T16_2_gfblup_variances_all_5001_6000.rds")
+T16_2_gfblup_variances_all_6001_7000=readRDS(file="T16_2_gfblup_variances_all_6001_7000.rds")
+T16_2_gfblup_variances_all_7001_8000=readRDS(file="T16_2_gfblup_variances_all_7001_8000.rds")
+T16_2_gfblup_variances_all_8001_9000=readRDS(file="T16_2_gfblup_variances_all_8001_9000.rds")
+T16_2_gfblup_variances_all_9001_10000=readRDS(file="T16_2_gfblup_variances_all_9001_10000.rds")
+T16_2_gfblup_variances_all_10001_11000=readRDS(file="T16_2_gfblup_variances_all_10001_11000.rds")
+T16_2_gfblup_variances_all_11001_12419=readRDS(file="T16_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T16_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_2_gfblup_variances_all=rep(list(list()),cycles)
+T16_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_1_1000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_1001_2000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_2001_3000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_3001_4000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_4001_5000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_5001_6000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_6001_7000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_7001_8000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_8001_9000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_9001_10000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_10001_11000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_11001_12419[[r]])
+
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_1_1000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_1001_2000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_2001_3000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_3001_4000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_4001_5000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_5001_6000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_6001_7000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_7001_8000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_8001_9000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_9001_10000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_10001_11000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T16_2_gfblup_prediction_all,"T16_2_gfblup_prediction_all.rds")
+saveRDS(T16_2_gfblup_variances_all,"T16_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_3_gblup_prediction_all_1_1000=readRDS(file="T16_3_gblup_prediction_all_1_1000.rds")
+T16_3_gblup_prediction_all_1001_2000=readRDS(file="T16_3_gblup_prediction_all_1001_2000.rds")
+T16_3_gblup_prediction_all_2001_3000=readRDS(file="T16_3_gblup_prediction_all_2001_3000.rds")
+T16_3_gblup_prediction_all_3001_4000=readRDS(file="T16_3_gblup_prediction_all_3001_4000.rds")
+T16_3_gblup_prediction_all_4001_5000=readRDS(file="T16_3_gblup_prediction_all_4001_5000.rds")
+T16_3_gblup_prediction_all_5001_6000=readRDS(file="T16_3_gblup_prediction_all_5001_6000.rds")
+T16_3_gblup_prediction_all_6001_7000=readRDS(file="T16_3_gblup_prediction_all_6001_7000.rds")
+T16_3_gblup_prediction_all_7001_8000=readRDS(file="T16_3_gblup_prediction_all_7001_8000.rds")
+T16_3_gblup_prediction_all_8001_9000=readRDS(file="T16_3_gblup_prediction_all_8001_9000.rds")
+T16_3_gblup_prediction_all_9001_10000=readRDS(file="T16_3_gblup_prediction_all_9001_10000.rds")
+T16_3_gblup_prediction_all_10001_11000=readRDS(file="T16_3_gblup_prediction_all_10001_11000.rds")
+T16_3_gblup_prediction_all_11001_12419=readRDS(file="T16_3_gblup_prediction_all_11001_12419.rds")
+T16_3_gblup_prediction_all=c(T16_3_gblup_prediction_all_1_1000,T16_3_gblup_prediction_all_1001_2000,T16_3_gblup_prediction_all_2001_3000,T16_3_gblup_prediction_all_3001_4000,T16_3_gblup_prediction_all_4001_5000,T16_3_gblup_prediction_all_5001_6000,T16_3_gblup_prediction_all_6001_7000,T16_3_gblup_prediction_all_7001_8000,T16_3_gblup_prediction_all_8001_9000,T16_3_gblup_prediction_all_9001_10000,T16_3_gblup_prediction_all_10001_11000,T16_3_gblup_prediction_all_11001_12419)
+
+T16_3_gblup_variances_all_1_1000=readRDS(file="T16_3_gblup_variances_all_1_1000.rds")
+T16_3_gblup_variances_all_1001_2000=readRDS(file="T16_3_gblup_variances_all_1001_2000.rds")
+T16_3_gblup_variances_all_2001_3000=readRDS(file="T16_3_gblup_variances_all_2001_3000.rds")
+T16_3_gblup_variances_all_3001_4000=readRDS(file="T16_3_gblup_variances_all_3001_4000.rds")
+T16_3_gblup_variances_all_4001_5000=readRDS(file="T16_3_gblup_variances_all_4001_5000.rds")
+T16_3_gblup_variances_all_5001_6000=readRDS(file="T16_3_gblup_variances_all_5001_6000.rds")
+T16_3_gblup_variances_all_6001_7000=readRDS(file="T16_3_gblup_variances_all_6001_7000.rds")
+T16_3_gblup_variances_all_7001_8000=readRDS(file="T16_3_gblup_variances_all_7001_8000.rds")
+T16_3_gblup_variances_all_8001_9000=readRDS(file="T16_3_gblup_variances_all_8001_9000.rds")
+T16_3_gblup_variances_all_9001_10000=readRDS(file="T16_3_gblup_variances_all_9001_10000.rds")
+T16_3_gblup_variances_all_10001_11000=readRDS(file="T16_3_gblup_variances_all_10001_11000.rds")
+T16_3_gblup_variances_all_11001_12419=readRDS(file="T16_3_gblup_variances_all_11001_12419.rds")
+T16_3_gblup_variances_all=c(T16_3_gblup_variances_all_1_1000,T16_3_gblup_variances_all_1001_2000,T16_3_gblup_variances_all_2001_3000,T16_3_gblup_variances_all_3001_4000,T16_3_gblup_variances_all_4001_5000,T16_3_gblup_variances_all_5001_6000,T16_3_gblup_variances_all_6001_7000,T16_3_gblup_variances_all_7001_8000,T16_3_gblup_variances_all_8001_9000,T16_3_gblup_variances_all_9001_10000,T16_3_gblup_variances_all_10001_11000,T16_3_gblup_variances_all_11001_12419)
+
+saveRDS(T16_3_gblup_prediction_all,"T16_3_gblup_prediction_all.rds")
+saveRDS(T16_3_gblup_variances_all,"T16_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_3_gfblup_prediction_all_1_1000=readRDS(file="T16_3_gfblup_prediction_all_1_1000.rds")
+T16_3_gfblup_prediction_all_1001_2000=readRDS(file="T16_3_gfblup_prediction_all_1001_2000.rds")
+T16_3_gfblup_prediction_all_2001_3000=readRDS(file="T16_3_gfblup_prediction_all_2001_3000.rds")
+T16_3_gfblup_prediction_all_3001_4000=readRDS(file="T16_3_gfblup_prediction_all_3001_4000.rds")
+T16_3_gfblup_prediction_all_4001_5000=readRDS(file="T16_3_gfblup_prediction_all_4001_5000.rds")
+T16_3_gfblup_prediction_all_5001_6000=readRDS(file="T16_3_gfblup_prediction_all_5001_6000.rds")
+T16_3_gfblup_prediction_all_6001_7000=readRDS(file="T16_3_gfblup_prediction_all_6001_7000.rds")
+T16_3_gfblup_prediction_all_7001_8000=readRDS(file="T16_3_gfblup_prediction_all_7001_8000.rds")
+T16_3_gfblup_prediction_all_8001_9000=readRDS(file="T16_3_gfblup_prediction_all_8001_9000.rds")
+T16_3_gfblup_prediction_all_9001_10000=readRDS(file="T16_3_gfblup_prediction_all_9001_10000.rds")
+T16_3_gfblup_prediction_all_10001_11000=readRDS(file="T16_3_gfblup_prediction_all_10001_11000.rds")
+T16_3_gfblup_prediction_all_11001_12419=readRDS(file="T16_3_gfblup_prediction_all_11001_12419.rds")
+
+T16_3_gfblup_variances_all_1_1000=readRDS(file="T16_3_gfblup_variances_all_1_1000.rds")
+T16_3_gfblup_variances_all_1001_2000=readRDS(file="T16_3_gfblup_variances_all_1001_2000.rds")
+T16_3_gfblup_variances_all_2001_3000=readRDS(file="T16_3_gfblup_variances_all_2001_3000.rds")
+T16_3_gfblup_variances_all_3001_4000=readRDS(file="T16_3_gfblup_variances_all_3001_4000.rds")
+T16_3_gfblup_variances_all_4001_5000=readRDS(file="T16_3_gfblup_variances_all_4001_5000.rds")
+T16_3_gfblup_variances_all_5001_6000=readRDS(file="T16_3_gfblup_variances_all_5001_6000.rds")
+T16_3_gfblup_variances_all_6001_7000=readRDS(file="T16_3_gfblup_variances_all_6001_7000.rds")
+T16_3_gfblup_variances_all_7001_8000=readRDS(file="T16_3_gfblup_variances_all_7001_8000.rds")
+T16_3_gfblup_variances_all_8001_9000=readRDS(file="T16_3_gfblup_variances_all_8001_9000.rds")
+T16_3_gfblup_variances_all_9001_10000=readRDS(file="T16_3_gfblup_variances_all_9001_10000.rds")
+T16_3_gfblup_variances_all_10001_11000=readRDS(file="T16_3_gfblup_variances_all_10001_11000.rds")
+T16_3_gfblup_variances_all_11001_12419=readRDS(file="T16_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T16_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_3_gfblup_variances_all=rep(list(list()),cycles)
+T16_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_1_1000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_1001_2000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_2001_3000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_3001_4000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_4001_5000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_5001_6000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_6001_7000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_7001_8000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_8001_9000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_9001_10000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_10001_11000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_11001_12419[[r]])
+
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_1_1000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_1001_2000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_2001_3000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_3001_4000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_4001_5000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_5001_6000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_6001_7000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_7001_8000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_8001_9000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_9001_10000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_10001_11000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T16_3_gfblup_prediction_all,"T16_3_gfblup_prediction_all.rds")
+saveRDS(T16_3_gfblup_variances_all,"T16_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_4_gblup_prediction_all_1_1000=readRDS(file="T16_4_gblup_prediction_all_1_1000.rds")
+T16_4_gblup_prediction_all_1001_2000=readRDS(file="T16_4_gblup_prediction_all_1001_2000.rds")
+T16_4_gblup_prediction_all_2001_3000=readRDS(file="T16_4_gblup_prediction_all_2001_3000.rds")
+T16_4_gblup_prediction_all_3001_4000=readRDS(file="T16_4_gblup_prediction_all_3001_4000.rds")
+T16_4_gblup_prediction_all_4001_5000=readRDS(file="T16_4_gblup_prediction_all_4001_5000.rds")
+T16_4_gblup_prediction_all_5001_6000=readRDS(file="T16_4_gblup_prediction_all_5001_6000.rds")
+T16_4_gblup_prediction_all_6001_7000=readRDS(file="T16_4_gblup_prediction_all_6001_7000.rds")
+T16_4_gblup_prediction_all_7001_8000=readRDS(file="T16_4_gblup_prediction_all_7001_8000.rds")
+T16_4_gblup_prediction_all_8001_9000=readRDS(file="T16_4_gblup_prediction_all_8001_9000.rds")
+T16_4_gblup_prediction_all_9001_10000=readRDS(file="T16_4_gblup_prediction_all_9001_10000.rds")
+T16_4_gblup_prediction_all_10001_11000=readRDS(file="T16_4_gblup_prediction_all_10001_11000.rds")
+T16_4_gblup_prediction_all_11001_12419=readRDS(file="T16_4_gblup_prediction_all_11001_12419.rds")
+T16_4_gblup_prediction_all=c(T16_4_gblup_prediction_all_1_1000,T16_4_gblup_prediction_all_1001_2000,T16_4_gblup_prediction_all_2001_3000,T16_4_gblup_prediction_all_3001_4000,T16_4_gblup_prediction_all_4001_5000,T16_4_gblup_prediction_all_5001_6000,T16_4_gblup_prediction_all_6001_7000,T16_4_gblup_prediction_all_7001_8000,T16_4_gblup_prediction_all_8001_9000,T16_4_gblup_prediction_all_9001_10000,T16_4_gblup_prediction_all_10001_11000,T16_4_gblup_prediction_all_11001_12419)
+
+T16_4_gblup_variances_all_1_1000=readRDS(file="T16_4_gblup_variances_all_1_1000.rds")
+T16_4_gblup_variances_all_1001_2000=readRDS(file="T16_4_gblup_variances_all_1001_2000.rds")
+T16_4_gblup_variances_all_2001_3000=readRDS(file="T16_4_gblup_variances_all_2001_3000.rds")
+T16_4_gblup_variances_all_3001_4000=readRDS(file="T16_4_gblup_variances_all_3001_4000.rds")
+T16_4_gblup_variances_all_4001_5000=readRDS(file="T16_4_gblup_variances_all_4001_5000.rds")
+T16_4_gblup_variances_all_5001_6000=readRDS(file="T16_4_gblup_variances_all_5001_6000.rds")
+T16_4_gblup_variances_all_6001_7000=readRDS(file="T16_4_gblup_variances_all_6001_7000.rds")
+T16_4_gblup_variances_all_7001_8000=readRDS(file="T16_4_gblup_variances_all_7001_8000.rds")
+T16_4_gblup_variances_all_8001_9000=readRDS(file="T16_4_gblup_variances_all_8001_9000.rds")
+T16_4_gblup_variances_all_9001_10000=readRDS(file="T16_4_gblup_variances_all_9001_10000.rds")
+T16_4_gblup_variances_all_10001_11000=readRDS(file="T16_4_gblup_variances_all_10001_11000.rds")
+T16_4_gblup_variances_all_11001_12419=readRDS(file="T16_4_gblup_variances_all_11001_12419.rds")
+T16_4_gblup_variances_all=c(T16_4_gblup_variances_all_1_1000,T16_4_gblup_variances_all_1001_2000,T16_4_gblup_variances_all_2001_3000,T16_4_gblup_variances_all_3001_4000,T16_4_gblup_variances_all_4001_5000,T16_4_gblup_variances_all_5001_6000,T16_4_gblup_variances_all_6001_7000,T16_4_gblup_variances_all_7001_8000,T16_4_gblup_variances_all_8001_9000,T16_4_gblup_variances_all_9001_10000,T16_4_gblup_variances_all_10001_11000,T16_4_gblup_variances_all_11001_12419)
+
+saveRDS(T16_4_gblup_prediction_all,"T16_4_gblup_prediction_all.rds")
+saveRDS(T16_4_gblup_variances_all,"T16_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_4_gfblup_prediction_all_1_1000=readRDS(file="T16_4_gfblup_prediction_all_1_1000.rds")
+T16_4_gfblup_prediction_all_1001_2000=readRDS(file="T16_4_gfblup_prediction_all_1001_2000.rds")
+T16_4_gfblup_prediction_all_2001_3000=readRDS(file="T16_4_gfblup_prediction_all_2001_3000.rds")
+T16_4_gfblup_prediction_all_3001_4000=readRDS(file="T16_4_gfblup_prediction_all_3001_4000.rds")
+T16_4_gfblup_prediction_all_4001_5000=readRDS(file="T16_4_gfblup_prediction_all_4001_5000.rds")
+T16_4_gfblup_prediction_all_5001_6000=readRDS(file="T16_4_gfblup_prediction_all_5001_6000.rds")
+T16_4_gfblup_prediction_all_6001_7000=readRDS(file="T16_4_gfblup_prediction_all_6001_7000.rds")
+T16_4_gfblup_prediction_all_7001_8000=readRDS(file="T16_4_gfblup_prediction_all_7001_8000.rds")
+T16_4_gfblup_prediction_all_8001_9000=readRDS(file="T16_4_gfblup_prediction_all_8001_9000.rds")
+T16_4_gfblup_prediction_all_9001_10000=readRDS(file="T16_4_gfblup_prediction_all_9001_10000.rds")
+T16_4_gfblup_prediction_all_10001_11000=readRDS(file="T16_4_gfblup_prediction_all_10001_11000.rds")
+T16_4_gfblup_prediction_all_11001_12419=readRDS(file="T16_4_gfblup_prediction_all_11001_12419.rds")
+
+T16_4_gfblup_variances_all_1_1000=readRDS(file="T16_4_gfblup_variances_all_1_1000.rds")
+T16_4_gfblup_variances_all_1001_2000=readRDS(file="T16_4_gfblup_variances_all_1001_2000.rds")
+T16_4_gfblup_variances_all_2001_3000=readRDS(file="T16_4_gfblup_variances_all_2001_3000.rds")
+T16_4_gfblup_variances_all_3001_4000=readRDS(file="T16_4_gfblup_variances_all_3001_4000.rds")
+T16_4_gfblup_variances_all_4001_5000=readRDS(file="T16_4_gfblup_variances_all_4001_5000.rds")
+T16_4_gfblup_variances_all_5001_6000=readRDS(file="T16_4_gfblup_variances_all_5001_6000.rds")
+T16_4_gfblup_variances_all_6001_7000=readRDS(file="T16_4_gfblup_variances_all_6001_7000.rds")
+T16_4_gfblup_variances_all_7001_8000=readRDS(file="T16_4_gfblup_variances_all_7001_8000.rds")
+T16_4_gfblup_variances_all_8001_9000=readRDS(file="T16_4_gfblup_variances_all_8001_9000.rds")
+T16_4_gfblup_variances_all_9001_10000=readRDS(file="T16_4_gfblup_variances_all_9001_10000.rds")
+T16_4_gfblup_variances_all_10001_11000=readRDS(file="T16_4_gfblup_variances_all_10001_11000.rds")
+T16_4_gfblup_variances_all_11001_12419=readRDS(file="T16_4_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T16_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_4_gfblup_variances_all=rep(list(list()),cycles)
+T16_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_1_1000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_1001_2000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_2001_3000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_3001_4000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_4001_5000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_5001_6000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_6001_7000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_7001_8000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_8001_9000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_9001_10000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_10001_11000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_11001_12419[[r]])
+
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_1_1000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_1001_2000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_2001_3000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_3001_4000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_4001_5000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_5001_6000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_6001_7000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_7001_8000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_8001_9000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_9001_10000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_10001_11000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T16_4_gfblup_prediction_all,"T16_4_gfblup_prediction_all.rds")
+saveRDS(T16_4_gfblup_variances_all,"T16_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_5_gblup_prediction_all_1_1000=readRDS(file="T16_5_gblup_prediction_all_1_1000.rds")
+T16_5_gblup_prediction_all_1001_2000=readRDS(file="T16_5_gblup_prediction_all_1001_2000.rds")
+T16_5_gblup_prediction_all_2001_3000=readRDS(file="T16_5_gblup_prediction_all_2001_3000.rds")
+T16_5_gblup_prediction_all_3001_4000=readRDS(file="T16_5_gblup_prediction_all_3001_4000.rds")
+T16_5_gblup_prediction_all_4001_5000=readRDS(file="T16_5_gblup_prediction_all_4001_5000.rds")
+T16_5_gblup_prediction_all_5001_6000=readRDS(file="T16_5_gblup_prediction_all_5001_6000.rds")
+T16_5_gblup_prediction_all_6001_7000=readRDS(file="T16_5_gblup_prediction_all_6001_7000.rds")
+T16_5_gblup_prediction_all_7001_8000=readRDS(file="T16_5_gblup_prediction_all_7001_8000.rds")
+T16_5_gblup_prediction_all_8001_9000=readRDS(file="T16_5_gblup_prediction_all_8001_9000.rds")
+T16_5_gblup_prediction_all_9001_10000=readRDS(file="T16_5_gblup_prediction_all_9001_10000.rds")
+T16_5_gblup_prediction_all_10001_11000=readRDS(file="T16_5_gblup_prediction_all_10001_11000.rds")
+T16_5_gblup_prediction_all_11001_12419=readRDS(file="T16_5_gblup_prediction_all_11001_12419.rds")
+T16_5_gblup_prediction_all=c(T16_5_gblup_prediction_all_1_1000,T16_5_gblup_prediction_all_1001_2000,T16_5_gblup_prediction_all_2001_3000,T16_5_gblup_prediction_all_3001_4000,T16_5_gblup_prediction_all_4001_5000,T16_5_gblup_prediction_all_5001_6000,T16_5_gblup_prediction_all_6001_7000,T16_5_gblup_prediction_all_7001_8000,T16_5_gblup_prediction_all_8001_9000,T16_5_gblup_prediction_all_9001_10000,T16_5_gblup_prediction_all_10001_11000,T16_5_gblup_prediction_all_11001_12419)
+
+T16_5_gblup_variances_all_1_1000=readRDS(file="T16_5_gblup_variances_all_1_1000.rds")
+T16_5_gblup_variances_all_1001_2000=readRDS(file="T16_5_gblup_variances_all_1001_2000.rds")
+T16_5_gblup_variances_all_2001_3000=readRDS(file="T16_5_gblup_variances_all_2001_3000.rds")
+T16_5_gblup_variances_all_3001_4000=readRDS(file="T16_5_gblup_variances_all_3001_4000.rds")
+T16_5_gblup_variances_all_4001_5000=readRDS(file="T16_5_gblup_variances_all_4001_5000.rds")
+T16_5_gblup_variances_all_5001_6000=readRDS(file="T16_5_gblup_variances_all_5001_6000.rds")
+T16_5_gblup_variances_all_6001_7000=readRDS(file="T16_5_gblup_variances_all_6001_7000.rds")
+T16_5_gblup_variances_all_7001_8000=readRDS(file="T16_5_gblup_variances_all_7001_8000.rds")
+T16_5_gblup_variances_all_8001_9000=readRDS(file="T16_5_gblup_variances_all_8001_9000.rds")
+T16_5_gblup_variances_all_9001_10000=readRDS(file="T16_5_gblup_variances_all_9001_10000.rds")
+T16_5_gblup_variances_all_10001_11000=readRDS(file="T16_5_gblup_variances_all_10001_11000.rds")
+T16_5_gblup_variances_all_11001_12419=readRDS(file="T16_5_gblup_variances_all_11001_12419.rds")
+T16_5_gblup_variances_all=c(T16_5_gblup_variances_all_1_1000,T16_5_gblup_variances_all_1001_2000,T16_5_gblup_variances_all_2001_3000,T16_5_gblup_variances_all_3001_4000,T16_5_gblup_variances_all_4001_5000,T16_5_gblup_variances_all_5001_6000,T16_5_gblup_variances_all_6001_7000,T16_5_gblup_variances_all_7001_8000,T16_5_gblup_variances_all_8001_9000,T16_5_gblup_variances_all_9001_10000,T16_5_gblup_variances_all_10001_11000,T16_5_gblup_variances_all_11001_12419)
+
+saveRDS(T16_5_gblup_prediction_all,"T16_5_gblup_prediction_all.rds")
+saveRDS(T16_5_gblup_variances_all,"T16_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_5_gfblup_prediction_all_1_1000=readRDS(file="T16_5_gfblup_prediction_all_1_1000.rds")
+T16_5_gfblup_prediction_all_1001_2000=readRDS(file="T16_5_gfblup_prediction_all_1001_2000.rds")
+T16_5_gfblup_prediction_all_2001_3000=readRDS(file="T16_5_gfblup_prediction_all_2001_3000.rds")
+T16_5_gfblup_prediction_all_3001_4000=readRDS(file="T16_5_gfblup_prediction_all_3001_4000.rds")
+T16_5_gfblup_prediction_all_4001_5000=readRDS(file="T16_5_gfblup_prediction_all_4001_5000.rds")
+T16_5_gfblup_prediction_all_5001_6000=readRDS(file="T16_5_gfblup_prediction_all_5001_6000.rds")
+T16_5_gfblup_prediction_all_6001_7000=readRDS(file="T16_5_gfblup_prediction_all_6001_7000.rds")
+T16_5_gfblup_prediction_all_7001_8000=readRDS(file="T16_5_gfblup_prediction_all_7001_8000.rds")
+T16_5_gfblup_prediction_all_8001_9000=readRDS(file="T16_5_gfblup_prediction_all_8001_9000.rds")
+T16_5_gfblup_prediction_all_9001_10000=readRDS(file="T16_5_gfblup_prediction_all_9001_10000.rds")
+T16_5_gfblup_prediction_all_10001_11000=readRDS(file="T16_5_gfblup_prediction_all_10001_11000.rds")
+T16_5_gfblup_prediction_all_11001_12419=readRDS(file="T16_5_gfblup_prediction_all_11001_12419.rds")
+
+T16_5_gfblup_variances_all_1_1000=readRDS(file="T16_5_gfblup_variances_all_1_1000.rds")
+T16_5_gfblup_variances_all_1001_2000=readRDS(file="T16_5_gfblup_variances_all_1001_2000.rds")
+T16_5_gfblup_variances_all_2001_3000=readRDS(file="T16_5_gfblup_variances_all_2001_3000.rds")
+T16_5_gfblup_variances_all_3001_4000=readRDS(file="T16_5_gfblup_variances_all_3001_4000.rds")
+T16_5_gfblup_variances_all_4001_5000=readRDS(file="T16_5_gfblup_variances_all_4001_5000.rds")
+T16_5_gfblup_variances_all_5001_6000=readRDS(file="T16_5_gfblup_variances_all_5001_6000.rds")
+T16_5_gfblup_variances_all_6001_7000=readRDS(file="T16_5_gfblup_variances_all_6001_7000.rds")
+T16_5_gfblup_variances_all_7001_8000=readRDS(file="T16_5_gfblup_variances_all_7001_8000.rds")
+T16_5_gfblup_variances_all_8001_9000=readRDS(file="T16_5_gfblup_variances_all_8001_9000.rds")
+T16_5_gfblup_variances_all_9001_10000=readRDS(file="T16_5_gfblup_variances_all_9001_10000.rds")
+T16_5_gfblup_variances_all_10001_11000=readRDS(file="T16_5_gfblup_variances_all_10001_11000.rds")
+T16_5_gfblup_variances_all_11001_12419=readRDS(file="T16_5_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T16_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_5_gfblup_variances_all=rep(list(list()),cycles)
+T16_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_1_1000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_1001_2000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_2001_3000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_3001_4000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_4001_5000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_5001_6000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_6001_7000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_7001_8000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_8001_9000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_9001_10000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_10001_11000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_11001_12419[[r]])
+
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_1_1000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_1001_2000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_2001_3000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_3001_4000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_4001_5000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_5001_6000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_6001_7000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_7001_8000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_8001_9000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_9001_10000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_10001_11000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T16_5_gfblup_prediction_all,"T16_5_gfblup_prediction_all.rds")
+saveRDS(T16_5_gfblup_variances_all,"T16_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_6_gblup_prediction_all_1_1000=readRDS(file="T16_6_gblup_prediction_all_1_1000.rds")
+T16_6_gblup_prediction_all_1001_2000=readRDS(file="T16_6_gblup_prediction_all_1001_2000.rds")
+T16_6_gblup_prediction_all_2001_3000=readRDS(file="T16_6_gblup_prediction_all_2001_3000.rds")
+T16_6_gblup_prediction_all_3001_4000=readRDS(file="T16_6_gblup_prediction_all_3001_4000.rds")
+T16_6_gblup_prediction_all_4001_5000=readRDS(file="T16_6_gblup_prediction_all_4001_5000.rds")
+T16_6_gblup_prediction_all_5001_6000=readRDS(file="T16_6_gblup_prediction_all_5001_6000.rds")
+T16_6_gblup_prediction_all_6001_7000=readRDS(file="T16_6_gblup_prediction_all_6001_7000.rds")
+T16_6_gblup_prediction_all_7001_8000=readRDS(file="T16_6_gblup_prediction_all_7001_8000.rds")
+T16_6_gblup_prediction_all_8001_9000=readRDS(file="T16_6_gblup_prediction_all_8001_9000.rds")
+T16_6_gblup_prediction_all_9001_10000=readRDS(file="T16_6_gblup_prediction_all_9001_10000.rds")
+T16_6_gblup_prediction_all_10001_11000=readRDS(file="T16_6_gblup_prediction_all_10001_11000.rds")
+T16_6_gblup_prediction_all_11001_12419=readRDS(file="T16_6_gblup_prediction_all_11001_12419.rds")
+T16_6_gblup_prediction_all=c(T16_6_gblup_prediction_all_1_1000,T16_6_gblup_prediction_all_1001_2000,T16_6_gblup_prediction_all_2001_3000,T16_6_gblup_prediction_all_3001_4000,T16_6_gblup_prediction_all_4001_5000,T16_6_gblup_prediction_all_5001_6000,T16_6_gblup_prediction_all_6001_7000,T16_6_gblup_prediction_all_7001_8000,T16_6_gblup_prediction_all_8001_9000,T16_6_gblup_prediction_all_9001_10000,T16_6_gblup_prediction_all_10001_11000,T16_6_gblup_prediction_all_11001_12419)
+
+T16_6_gblup_variances_all_1_1000=readRDS(file="T16_6_gblup_variances_all_1_1000.rds")
+T16_6_gblup_variances_all_1001_2000=readRDS(file="T16_6_gblup_variances_all_1001_2000.rds")
+T16_6_gblup_variances_all_2001_3000=readRDS(file="T16_6_gblup_variances_all_2001_3000.rds")
+T16_6_gblup_variances_all_3001_4000=readRDS(file="T16_6_gblup_variances_all_3001_4000.rds")
+T16_6_gblup_variances_all_4001_5000=readRDS(file="T16_6_gblup_variances_all_4001_5000.rds")
+T16_6_gblup_variances_all_5001_6000=readRDS(file="T16_6_gblup_variances_all_5001_6000.rds")
+T16_6_gblup_variances_all_6001_7000=readRDS(file="T16_6_gblup_variances_all_6001_7000.rds")
+T16_6_gblup_variances_all_7001_8000=readRDS(file="T16_6_gblup_variances_all_7001_8000.rds")
+T16_6_gblup_variances_all_8001_9000=readRDS(file="T16_6_gblup_variances_all_8001_9000.rds")
+T16_6_gblup_variances_all_9001_10000=readRDS(file="T16_6_gblup_variances_all_9001_10000.rds")
+T16_6_gblup_variances_all_10001_11000=readRDS(file="T16_6_gblup_variances_all_10001_11000.rds")
+T16_6_gblup_variances_all_11001_12419=readRDS(file="T16_6_gblup_variances_all_11001_12419.rds")
+T16_6_gblup_variances_all=c(T16_6_gblup_variances_all_1_1000,T16_6_gblup_variances_all_1001_2000,T16_6_gblup_variances_all_2001_3000,T16_6_gblup_variances_all_3001_4000,T16_6_gblup_variances_all_4001_5000,T16_6_gblup_variances_all_5001_6000,T16_6_gblup_variances_all_6001_7000,T16_6_gblup_variances_all_7001_8000,T16_6_gblup_variances_all_8001_9000,T16_6_gblup_variances_all_9001_10000,T16_6_gblup_variances_all_10001_11000,T16_6_gblup_variances_all_11001_12419)
+
+saveRDS(T16_6_gblup_prediction_all,"T16_6_gblup_prediction_all.rds")
+saveRDS(T16_6_gblup_variances_all,"T16_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_6_gfblup_prediction_all_1_1000=readRDS(file="T16_6_gfblup_prediction_all_1_1000.rds")
+T16_6_gfblup_prediction_all_1001_2000=readRDS(file="T16_6_gfblup_prediction_all_1001_2000.rds")
+T16_6_gfblup_prediction_all_2001_3000=readRDS(file="T16_6_gfblup_prediction_all_2001_3000.rds")
+T16_6_gfblup_prediction_all_3001_4000=readRDS(file="T16_6_gfblup_prediction_all_3001_4000.rds")
+T16_6_gfblup_prediction_all_4001_5000=readRDS(file="T16_6_gfblup_prediction_all_4001_5000.rds")
+T16_6_gfblup_prediction_all_5001_6000=readRDS(file="T16_6_gfblup_prediction_all_5001_6000.rds")
+T16_6_gfblup_prediction_all_6001_7000=readRDS(file="T16_6_gfblup_prediction_all_6001_7000.rds")
+T16_6_gfblup_prediction_all_7001_8000=readRDS(file="T16_6_gfblup_prediction_all_7001_8000.rds")
+T16_6_gfblup_prediction_all_8001_9000=readRDS(file="T16_6_gfblup_prediction_all_8001_9000.rds")
+T16_6_gfblup_prediction_all_9001_10000=readRDS(file="T16_6_gfblup_prediction_all_9001_10000.rds")
+T16_6_gfblup_prediction_all_10001_11000=readRDS(file="T16_6_gfblup_prediction_all_10001_11000.rds")
+T16_6_gfblup_prediction_all_11001_12419=readRDS(file="T16_6_gfblup_prediction_all_11001_12419.rds")
+
+T16_6_gfblup_variances_all_1_1000=readRDS(file="T16_6_gfblup_variances_all_1_1000.rds")
+T16_6_gfblup_variances_all_1001_2000=readRDS(file="T16_6_gfblup_variances_all_1001_2000.rds")
+T16_6_gfblup_variances_all_2001_3000=readRDS(file="T16_6_gfblup_variances_all_2001_3000.rds")
+T16_6_gfblup_variances_all_3001_4000=readRDS(file="T16_6_gfblup_variances_all_3001_4000.rds")
+T16_6_gfblup_variances_all_4001_5000=readRDS(file="T16_6_gfblup_variances_all_4001_5000.rds")
+T16_6_gfblup_variances_all_5001_6000=readRDS(file="T16_6_gfblup_variances_all_5001_6000.rds")
+T16_6_gfblup_variances_all_6001_7000=readRDS(file="T16_6_gfblup_variances_all_6001_7000.rds")
+T16_6_gfblup_variances_all_7001_8000=readRDS(file="T16_6_gfblup_variances_all_7001_8000.rds")
+T16_6_gfblup_variances_all_8001_9000=readRDS(file="T16_6_gfblup_variances_all_8001_9000.rds")
+T16_6_gfblup_variances_all_9001_10000=readRDS(file="T16_6_gfblup_variances_all_9001_10000.rds")
+T16_6_gfblup_variances_all_10001_11000=readRDS(file="T16_6_gfblup_variances_all_10001_11000.rds")
+T16_6_gfblup_variances_all_11001_12419=readRDS(file="T16_6_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T16_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_6_gfblup_variances_all=rep(list(list()),cycles)
+T16_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_1_1000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_1001_2000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_2001_3000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_3001_4000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_4001_5000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_5001_6000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_6001_7000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_7001_8000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_8001_9000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_9001_10000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_10001_11000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_11001_12419[[r]])
+
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_1_1000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_1001_2000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_2001_3000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_3001_4000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_4001_5000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_5001_6000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_6001_7000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_7001_8000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_8001_9000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_9001_10000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_10001_11000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T16_6_gfblup_prediction_all,"T16_6_gfblup_prediction_all.rds")
+saveRDS(T16_6_gfblup_variances_all,"T16_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_7_gblup_prediction_all_1_1000=readRDS(file="T16_7_gblup_prediction_all_1_1000.rds")
+T16_7_gblup_prediction_all_1001_2000=readRDS(file="T16_7_gblup_prediction_all_1001_2000.rds")
+T16_7_gblup_prediction_all_2001_3000=readRDS(file="T16_7_gblup_prediction_all_2001_3000.rds")
+T16_7_gblup_prediction_all_3001_4000=readRDS(file="T16_7_gblup_prediction_all_3001_4000.rds")
+T16_7_gblup_prediction_all_4001_5000=readRDS(file="T16_7_gblup_prediction_all_4001_5000.rds")
+T16_7_gblup_prediction_all_5001_6000=readRDS(file="T16_7_gblup_prediction_all_5001_6000.rds")
+T16_7_gblup_prediction_all_6001_7000=readRDS(file="T16_7_gblup_prediction_all_6001_7000.rds")
+T16_7_gblup_prediction_all_7001_8000=readRDS(file="T16_7_gblup_prediction_all_7001_8000.rds")
+T16_7_gblup_prediction_all_8001_9000=readRDS(file="T16_7_gblup_prediction_all_8001_9000.rds")
+T16_7_gblup_prediction_all_9001_10000=readRDS(file="T16_7_gblup_prediction_all_9001_10000.rds")
+T16_7_gblup_prediction_all_10001_11000=readRDS(file="T16_7_gblup_prediction_all_10001_11000.rds")
+T16_7_gblup_prediction_all_11001_12419=readRDS(file="T16_7_gblup_prediction_all_11001_12419.rds")
+T16_7_gblup_prediction_all=c(T16_7_gblup_prediction_all_1_1000,T16_7_gblup_prediction_all_1001_2000,T16_7_gblup_prediction_all_2001_3000,T16_7_gblup_prediction_all_3001_4000,T16_7_gblup_prediction_all_4001_5000,T16_7_gblup_prediction_all_5001_6000,T16_7_gblup_prediction_all_6001_7000,T16_7_gblup_prediction_all_7001_8000,T16_7_gblup_prediction_all_8001_9000,T16_7_gblup_prediction_all_9001_10000,T16_7_gblup_prediction_all_10001_11000,T16_7_gblup_prediction_all_11001_12419)
+
+T16_7_gblup_variances_all_1_1000=readRDS(file="T16_7_gblup_variances_all_1_1000.rds")
+T16_7_gblup_variances_all_1001_2000=readRDS(file="T16_7_gblup_variances_all_1001_2000.rds")
+T16_7_gblup_variances_all_2001_3000=readRDS(file="T16_7_gblup_variances_all_2001_3000.rds")
+T16_7_gblup_variances_all_3001_4000=readRDS(file="T16_7_gblup_variances_all_3001_4000.rds")
+T16_7_gblup_variances_all_4001_5000=readRDS(file="T16_7_gblup_variances_all_4001_5000.rds")
+T16_7_gblup_variances_all_5001_6000=readRDS(file="T16_7_gblup_variances_all_5001_6000.rds")
+T16_7_gblup_variances_all_6001_7000=readRDS(file="T16_7_gblup_variances_all_6001_7000.rds")
+T16_7_gblup_variances_all_7001_8000=readRDS(file="T16_7_gblup_variances_all_7001_8000.rds")
+T16_7_gblup_variances_all_8001_9000=readRDS(file="T16_7_gblup_variances_all_8001_9000.rds")
+T16_7_gblup_variances_all_9001_10000=readRDS(file="T16_7_gblup_variances_all_9001_10000.rds")
+T16_7_gblup_variances_all_10001_11000=readRDS(file="T16_7_gblup_variances_all_10001_11000.rds")
+T16_7_gblup_variances_all_11001_12419=readRDS(file="T16_7_gblup_variances_all_11001_12419.rds")
+T16_7_gblup_variances_all=c(T16_7_gblup_variances_all_1_1000,T16_7_gblup_variances_all_1001_2000,T16_7_gblup_variances_all_2001_3000,T16_7_gblup_variances_all_3001_4000,T16_7_gblup_variances_all_4001_5000,T16_7_gblup_variances_all_5001_6000,T16_7_gblup_variances_all_6001_7000,T16_7_gblup_variances_all_7001_8000,T16_7_gblup_variances_all_8001_9000,T16_7_gblup_variances_all_9001_10000,T16_7_gblup_variances_all_10001_11000,T16_7_gblup_variances_all_11001_12419)
+
+saveRDS(T16_7_gblup_prediction_all,"T16_7_gblup_prediction_all.rds")
+saveRDS(T16_7_gblup_variances_all,"T16_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_7_gfblup_prediction_all_1_1000=readRDS(file="T16_7_gfblup_prediction_all_1_1000.rds")
+T16_7_gfblup_prediction_all_1001_2000=readRDS(file="T16_7_gfblup_prediction_all_1001_2000.rds")
+T16_7_gfblup_prediction_all_2001_3000=readRDS(file="T16_7_gfblup_prediction_all_2001_3000.rds")
+T16_7_gfblup_prediction_all_3001_4000=readRDS(file="T16_7_gfblup_prediction_all_3001_4000.rds")
+T16_7_gfblup_prediction_all_4001_5000=readRDS(file="T16_7_gfblup_prediction_all_4001_5000.rds")
+T16_7_gfblup_prediction_all_5001_6000=readRDS(file="T16_7_gfblup_prediction_all_5001_6000.rds")
+T16_7_gfblup_prediction_all_6001_7000=readRDS(file="T16_7_gfblup_prediction_all_6001_7000.rds")
+T16_7_gfblup_prediction_all_7001_8000=readRDS(file="T16_7_gfblup_prediction_all_7001_8000.rds")
+T16_7_gfblup_prediction_all_8001_9000=readRDS(file="T16_7_gfblup_prediction_all_8001_9000.rds")
+T16_7_gfblup_prediction_all_9001_10000=readRDS(file="T16_7_gfblup_prediction_all_9001_10000.rds")
+T16_7_gfblup_prediction_all_10001_11000=readRDS(file="T16_7_gfblup_prediction_all_10001_11000.rds")
+T16_7_gfblup_prediction_all_11001_12419=readRDS(file="T16_7_gfblup_prediction_all_11001_12419.rds")
+
+T16_7_gfblup_variances_all_1_1000=readRDS(file="T16_7_gfblup_variances_all_1_1000.rds")
+T16_7_gfblup_variances_all_1001_2000=readRDS(file="T16_7_gfblup_variances_all_1001_2000.rds")
+T16_7_gfblup_variances_all_2001_3000=readRDS(file="T16_7_gfblup_variances_all_2001_3000.rds")
+T16_7_gfblup_variances_all_3001_4000=readRDS(file="T16_7_gfblup_variances_all_3001_4000.rds")
+T16_7_gfblup_variances_all_4001_5000=readRDS(file="T16_7_gfblup_variances_all_4001_5000.rds")
+T16_7_gfblup_variances_all_5001_6000=readRDS(file="T16_7_gfblup_variances_all_5001_6000.rds")
+T16_7_gfblup_variances_all_6001_7000=readRDS(file="T16_7_gfblup_variances_all_6001_7000.rds")
+T16_7_gfblup_variances_all_7001_8000=readRDS(file="T16_7_gfblup_variances_all_7001_8000.rds")
+T16_7_gfblup_variances_all_8001_9000=readRDS(file="T16_7_gfblup_variances_all_8001_9000.rds")
+T16_7_gfblup_variances_all_9001_10000=readRDS(file="T16_7_gfblup_variances_all_9001_10000.rds")
+T16_7_gfblup_variances_all_10001_11000=readRDS(file="T16_7_gfblup_variances_all_10001_11000.rds")
+T16_7_gfblup_variances_all_11001_12419=readRDS(file="T16_7_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T16_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_7_gfblup_variances_all=rep(list(list()),cycles)
+T16_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_1_1000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_1001_2000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_2001_3000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_3001_4000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_4001_5000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_5001_6000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_6001_7000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_7001_8000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_8001_9000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_9001_10000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_10001_11000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_11001_12419[[r]])
+
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_1_1000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_1001_2000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_2001_3000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_3001_4000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_4001_5000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_5001_6000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_6001_7000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_7001_8000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_8001_9000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_9001_10000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_10001_11000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T16_7_gfblup_prediction_all,"T16_7_gfblup_prediction_all.rds")
+saveRDS(T16_7_gfblup_variances_all,"T16_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_8_gblup_prediction_all_1_1000=readRDS(file="T16_8_gblup_prediction_all_1_1000.rds")
+T16_8_gblup_prediction_all_1001_2000=readRDS(file="T16_8_gblup_prediction_all_1001_2000.rds")
+T16_8_gblup_prediction_all_2001_3000=readRDS(file="T16_8_gblup_prediction_all_2001_3000.rds")
+T16_8_gblup_prediction_all_3001_4000=readRDS(file="T16_8_gblup_prediction_all_3001_4000.rds")
+T16_8_gblup_prediction_all_4001_5000=readRDS(file="T16_8_gblup_prediction_all_4001_5000.rds")
+T16_8_gblup_prediction_all_5001_6000=readRDS(file="T16_8_gblup_prediction_all_5001_6000.rds")
+T16_8_gblup_prediction_all_6001_7000=readRDS(file="T16_8_gblup_prediction_all_6001_7000.rds")
+T16_8_gblup_prediction_all_7001_8000=readRDS(file="T16_8_gblup_prediction_all_7001_8000.rds")
+T16_8_gblup_prediction_all_8001_9000=readRDS(file="T16_8_gblup_prediction_all_8001_9000.rds")
+T16_8_gblup_prediction_all_9001_10000=readRDS(file="T16_8_gblup_prediction_all_9001_10000.rds")
+T16_8_gblup_prediction_all_10001_11000=readRDS(file="T16_8_gblup_prediction_all_10001_11000.rds")
+T16_8_gblup_prediction_all_11001_12419=readRDS(file="T16_8_gblup_prediction_all_11001_12419.rds")
+T16_8_gblup_prediction_all=c(T16_8_gblup_prediction_all_1_1000,T16_8_gblup_prediction_all_1001_2000,T16_8_gblup_prediction_all_2001_3000,T16_8_gblup_prediction_all_3001_4000,T16_8_gblup_prediction_all_4001_5000,T16_8_gblup_prediction_all_5001_6000,T16_8_gblup_prediction_all_6001_7000,T16_8_gblup_prediction_all_7001_8000,T16_8_gblup_prediction_all_8001_9000,T16_8_gblup_prediction_all_9001_10000,T16_8_gblup_prediction_all_10001_11000,T16_8_gblup_prediction_all_11001_12419)
+
+T16_8_gblup_variances_all_1_1000=readRDS(file="T16_8_gblup_variances_all_1_1000.rds")
+T16_8_gblup_variances_all_1001_2000=readRDS(file="T16_8_gblup_variances_all_1001_2000.rds")
+T16_8_gblup_variances_all_2001_3000=readRDS(file="T16_8_gblup_variances_all_2001_3000.rds")
+T16_8_gblup_variances_all_3001_4000=readRDS(file="T16_8_gblup_variances_all_3001_4000.rds")
+T16_8_gblup_variances_all_4001_5000=readRDS(file="T16_8_gblup_variances_all_4001_5000.rds")
+T16_8_gblup_variances_all_5001_6000=readRDS(file="T16_8_gblup_variances_all_5001_6000.rds")
+T16_8_gblup_variances_all_6001_7000=readRDS(file="T16_8_gblup_variances_all_6001_7000.rds")
+T16_8_gblup_variances_all_7001_8000=readRDS(file="T16_8_gblup_variances_all_7001_8000.rds")
+T16_8_gblup_variances_all_8001_9000=readRDS(file="T16_8_gblup_variances_all_8001_9000.rds")
+T16_8_gblup_variances_all_9001_10000=readRDS(file="T16_8_gblup_variances_all_9001_10000.rds")
+T16_8_gblup_variances_all_10001_11000=readRDS(file="T16_8_gblup_variances_all_10001_11000.rds")
+T16_8_gblup_variances_all_11001_12419=readRDS(file="T16_8_gblup_variances_all_11001_12419.rds")
+T16_8_gblup_variances_all=c(T16_8_gblup_variances_all_1_1000,T16_8_gblup_variances_all_1001_2000,T16_8_gblup_variances_all_2001_3000,T16_8_gblup_variances_all_3001_4000,T16_8_gblup_variances_all_4001_5000,T16_8_gblup_variances_all_5001_6000,T16_8_gblup_variances_all_6001_7000,T16_8_gblup_variances_all_7001_8000,T16_8_gblup_variances_all_8001_9000,T16_8_gblup_variances_all_9001_10000,T16_8_gblup_variances_all_10001_11000,T16_8_gblup_variances_all_11001_12419)
+
+saveRDS(T16_8_gblup_prediction_all,"T16_8_gblup_prediction_all.rds")
+saveRDS(T16_8_gblup_variances_all,"T16_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_8_gfblup_prediction_all_1_1000=readRDS(file="T16_8_gfblup_prediction_all_1_1000.rds")
+T16_8_gfblup_prediction_all_1001_2000=readRDS(file="T16_8_gfblup_prediction_all_1001_2000.rds")
+T16_8_gfblup_prediction_all_2001_3000=readRDS(file="T16_8_gfblup_prediction_all_2001_3000.rds")
+T16_8_gfblup_prediction_all_3001_4000=readRDS(file="T16_8_gfblup_prediction_all_3001_4000.rds")
+T16_8_gfblup_prediction_all_4001_5000=readRDS(file="T16_8_gfblup_prediction_all_4001_5000.rds")
+T16_8_gfblup_prediction_all_5001_6000=readRDS(file="T16_8_gfblup_prediction_all_5001_6000.rds")
+T16_8_gfblup_prediction_all_6001_7000=readRDS(file="T16_8_gfblup_prediction_all_6001_7000.rds")
+T16_8_gfblup_prediction_all_7001_8000=readRDS(file="T16_8_gfblup_prediction_all_7001_8000.rds")
+T16_8_gfblup_prediction_all_8001_9000=readRDS(file="T16_8_gfblup_prediction_all_8001_9000.rds")
+T16_8_gfblup_prediction_all_9001_10000=readRDS(file="T16_8_gfblup_prediction_all_9001_10000.rds")
+T16_8_gfblup_prediction_all_10001_11000=readRDS(file="T16_8_gfblup_prediction_all_10001_11000.rds")
+T16_8_gfblup_prediction_all_11001_12419=readRDS(file="T16_8_gfblup_prediction_all_11001_12419.rds")
+
+T16_8_gfblup_variances_all_1_1000=readRDS(file="T16_8_gfblup_variances_all_1_1000.rds")
+T16_8_gfblup_variances_all_1001_2000=readRDS(file="T16_8_gfblup_variances_all_1001_2000.rds")
+T16_8_gfblup_variances_all_2001_3000=readRDS(file="T16_8_gfblup_variances_all_2001_3000.rds")
+T16_8_gfblup_variances_all_3001_4000=readRDS(file="T16_8_gfblup_variances_all_3001_4000.rds")
+T16_8_gfblup_variances_all_4001_5000=readRDS(file="T16_8_gfblup_variances_all_4001_5000.rds")
+T16_8_gfblup_variances_all_5001_6000=readRDS(file="T16_8_gfblup_variances_all_5001_6000.rds")
+T16_8_gfblup_variances_all_6001_7000=readRDS(file="T16_8_gfblup_variances_all_6001_7000.rds")
+T16_8_gfblup_variances_all_7001_8000=readRDS(file="T16_8_gfblup_variances_all_7001_8000.rds")
+T16_8_gfblup_variances_all_8001_9000=readRDS(file="T16_8_gfblup_variances_all_8001_9000.rds")
+T16_8_gfblup_variances_all_9001_10000=readRDS(file="T16_8_gfblup_variances_all_9001_10000.rds")
+T16_8_gfblup_variances_all_10001_11000=readRDS(file="T16_8_gfblup_variances_all_10001_11000.rds")
+T16_8_gfblup_variances_all_11001_12419=readRDS(file="T16_8_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T16_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_8_gfblup_variances_all=rep(list(list()),cycles)
+T16_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_1_1000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_1001_2000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_2001_3000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_3001_4000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_4001_5000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_5001_6000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_6001_7000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_7001_8000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_8001_9000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_9001_10000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_10001_11000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_11001_12419[[r]])
+
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_1_1000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_1001_2000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_2001_3000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_3001_4000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_4001_5000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_5001_6000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_6001_7000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_7001_8000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_8001_9000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_9001_10000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_10001_11000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T16_8_gfblup_prediction_all,"T16_8_gfblup_prediction_all.rds")
+saveRDS(T16_8_gfblup_variances_all,"T16_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_1_gblup_prediction_all_1_1000=readRDS(file="T17_1_gblup_prediction_all_1_1000.rds")
+T17_1_gblup_prediction_all_1001_2000=readRDS(file="T17_1_gblup_prediction_all_1001_2000.rds")
+T17_1_gblup_prediction_all_2001_3000=readRDS(file="T17_1_gblup_prediction_all_2001_3000.rds")
+T17_1_gblup_prediction_all_3001_4000=readRDS(file="T17_1_gblup_prediction_all_3001_4000.rds")
+T17_1_gblup_prediction_all_4001_5000=readRDS(file="T17_1_gblup_prediction_all_4001_5000.rds")
+T17_1_gblup_prediction_all_5001_6000=readRDS(file="T17_1_gblup_prediction_all_5001_6000.rds")
+T17_1_gblup_prediction_all_6001_7000=readRDS(file="T17_1_gblup_prediction_all_6001_7000.rds")
+T17_1_gblup_prediction_all_7001_8000=readRDS(file="T17_1_gblup_prediction_all_7001_8000.rds")
+T17_1_gblup_prediction_all_8001_9000=readRDS(file="T17_1_gblup_prediction_all_8001_9000.rds")
+T17_1_gblup_prediction_all_9001_10000=readRDS(file="T17_1_gblup_prediction_all_9001_10000.rds")
+T17_1_gblup_prediction_all_10001_11000=readRDS(file="T17_1_gblup_prediction_all_10001_11000.rds")
+T17_1_gblup_prediction_all_11001_12419=readRDS(file="T17_1_gblup_prediction_all_11001_12419.rds")
+T17_1_gblup_prediction_all=c(T17_1_gblup_prediction_all_1_1000,T17_1_gblup_prediction_all_1001_2000,T17_1_gblup_prediction_all_2001_3000,T17_1_gblup_prediction_all_3001_4000,T17_1_gblup_prediction_all_4001_5000,T17_1_gblup_prediction_all_5001_6000,T17_1_gblup_prediction_all_6001_7000,T17_1_gblup_prediction_all_7001_8000,T17_1_gblup_prediction_all_8001_9000,T17_1_gblup_prediction_all_9001_10000,T17_1_gblup_prediction_all_10001_11000,T17_1_gblup_prediction_all_11001_12419)
+
+T17_1_gblup_variances_all_1_1000=readRDS(file="T17_1_gblup_variances_all_1_1000.rds")
+T17_1_gblup_variances_all_1001_2000=readRDS(file="T17_1_gblup_variances_all_1001_2000.rds")
+T17_1_gblup_variances_all_2001_3000=readRDS(file="T17_1_gblup_variances_all_2001_3000.rds")
+T17_1_gblup_variances_all_3001_4000=readRDS(file="T17_1_gblup_variances_all_3001_4000.rds")
+T17_1_gblup_variances_all_4001_5000=readRDS(file="T17_1_gblup_variances_all_4001_5000.rds")
+T17_1_gblup_variances_all_5001_6000=readRDS(file="T17_1_gblup_variances_all_5001_6000.rds")
+T17_1_gblup_variances_all_6001_7000=readRDS(file="T17_1_gblup_variances_all_6001_7000.rds")
+T17_1_gblup_variances_all_7001_8000=readRDS(file="T17_1_gblup_variances_all_7001_8000.rds")
+T17_1_gblup_variances_all_8001_9000=readRDS(file="T17_1_gblup_variances_all_8001_9000.rds")
+T17_1_gblup_variances_all_9001_10000=readRDS(file="T17_1_gblup_variances_all_9001_10000.rds")
+T17_1_gblup_variances_all_10001_11000=readRDS(file="T17_1_gblup_variances_all_10001_11000.rds")
+T17_1_gblup_variances_all_11001_12419=readRDS(file="T17_1_gblup_variances_all_11001_12419.rds")
+T17_1_gblup_variances_all=c(T17_1_gblup_variances_all_1_1000,T17_1_gblup_variances_all_1001_2000,T17_1_gblup_variances_all_2001_3000,T17_1_gblup_variances_all_3001_4000,T17_1_gblup_variances_all_4001_5000,T17_1_gblup_variances_all_5001_6000,T17_1_gblup_variances_all_6001_7000,T17_1_gblup_variances_all_7001_8000,T17_1_gblup_variances_all_8001_9000,T17_1_gblup_variances_all_9001_10000,T17_1_gblup_variances_all_10001_11000,T17_1_gblup_variances_all_11001_12419)
+
+saveRDS(T17_1_gblup_prediction_all,"T17_1_gblup_prediction_all.rds")
+saveRDS(T17_1_gblup_variances_all,"T17_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_1_gfblup_prediction_all_1_1000=readRDS(file="T17_1_gfblup_prediction_all_1_1000.rds")
+T17_1_gfblup_prediction_all_1001_2000=readRDS(file="T17_1_gfblup_prediction_all_1001_2000.rds")
+T17_1_gfblup_prediction_all_2001_3000=readRDS(file="T17_1_gfblup_prediction_all_2001_3000.rds")
+T17_1_gfblup_prediction_all_3001_4000=readRDS(file="T17_1_gfblup_prediction_all_3001_4000.rds")
+T17_1_gfblup_prediction_all_4001_5000=readRDS(file="T17_1_gfblup_prediction_all_4001_5000.rds")
+T17_1_gfblup_prediction_all_5001_6000=readRDS(file="T17_1_gfblup_prediction_all_5001_6000.rds")
+T17_1_gfblup_prediction_all_6001_7000=readRDS(file="T17_1_gfblup_prediction_all_6001_7000.rds")
+T17_1_gfblup_prediction_all_7001_8000=readRDS(file="T17_1_gfblup_prediction_all_7001_8000.rds")
+T17_1_gfblup_prediction_all_8001_9000=readRDS(file="T17_1_gfblup_prediction_all_8001_9000.rds")
+T17_1_gfblup_prediction_all_9001_10000=readRDS(file="T17_1_gfblup_prediction_all_9001_10000.rds")
+T17_1_gfblup_prediction_all_10001_11000=readRDS(file="T17_1_gfblup_prediction_all_10001_11000.rds")
+T17_1_gfblup_prediction_all_11001_12419=readRDS(file="T17_1_gfblup_prediction_all_11001_12419.rds")
+
+T17_1_gfblup_variances_all_1_1000=readRDS(file="T17_1_gfblup_variances_all_1_1000.rds")
+T17_1_gfblup_variances_all_1001_2000=readRDS(file="T17_1_gfblup_variances_all_1001_2000.rds")
+T17_1_gfblup_variances_all_2001_3000=readRDS(file="T17_1_gfblup_variances_all_2001_3000.rds")
+T17_1_gfblup_variances_all_3001_4000=readRDS(file="T17_1_gfblup_variances_all_3001_4000.rds")
+T17_1_gfblup_variances_all_4001_5000=readRDS(file="T17_1_gfblup_variances_all_4001_5000.rds")
+T17_1_gfblup_variances_all_5001_6000=readRDS(file="T17_1_gfblup_variances_all_5001_6000.rds")
+T17_1_gfblup_variances_all_6001_7000=readRDS(file="T17_1_gfblup_variances_all_6001_7000.rds")
+T17_1_gfblup_variances_all_7001_8000=readRDS(file="T17_1_gfblup_variances_all_7001_8000.rds")
+T17_1_gfblup_variances_all_8001_9000=readRDS(file="T17_1_gfblup_variances_all_8001_9000.rds")
+T17_1_gfblup_variances_all_9001_10000=readRDS(file="T17_1_gfblup_variances_all_9001_10000.rds")
+T17_1_gfblup_variances_all_10001_11000=readRDS(file="T17_1_gfblup_variances_all_10001_11000.rds")
+T17_1_gfblup_variances_all_11001_12419=readRDS(file="T17_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T17_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_1_gfblup_variances_all=rep(list(list()),cycles)
+T17_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_1_1000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_1001_2000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_2001_3000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_3001_4000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_4001_5000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_5001_6000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_6001_7000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_7001_8000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_8001_9000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_9001_10000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_10001_11000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_11001_12419[[r]])
+
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_1_1000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_1001_2000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_2001_3000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_3001_4000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_4001_5000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_5001_6000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_6001_7000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_7001_8000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_8001_9000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_9001_10000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_10001_11000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T17_1_gfblup_prediction_all,"T17_1_gfblup_prediction_all.rds")
+saveRDS(T17_1_gfblup_variances_all,"T17_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_2_gblup_prediction_all_1_1000=readRDS(file="T17_2_gblup_prediction_all_1_1000.rds")
+T17_2_gblup_prediction_all_1001_2000=readRDS(file="T17_2_gblup_prediction_all_1001_2000.rds")
+T17_2_gblup_prediction_all_2001_3000=readRDS(file="T17_2_gblup_prediction_all_2001_3000.rds")
+T17_2_gblup_prediction_all_3001_4000=readRDS(file="T17_2_gblup_prediction_all_3001_4000.rds")
+T17_2_gblup_prediction_all_4001_5000=readRDS(file="T17_2_gblup_prediction_all_4001_5000.rds")
+T17_2_gblup_prediction_all_5001_6000=readRDS(file="T17_2_gblup_prediction_all_5001_6000.rds")
+T17_2_gblup_prediction_all_6001_7000=readRDS(file="T17_2_gblup_prediction_all_6001_7000.rds")
+T17_2_gblup_prediction_all_7001_8000=readRDS(file="T17_2_gblup_prediction_all_7001_8000.rds")
+T17_2_gblup_prediction_all_8001_9000=readRDS(file="T17_2_gblup_prediction_all_8001_9000.rds")
+T17_2_gblup_prediction_all_9001_10000=readRDS(file="T17_2_gblup_prediction_all_9001_10000.rds")
+T17_2_gblup_prediction_all_10001_11000=readRDS(file="T17_2_gblup_prediction_all_10001_11000.rds")
+T17_2_gblup_prediction_all_11001_12419=readRDS(file="T17_2_gblup_prediction_all_11001_12419.rds")
+T17_2_gblup_prediction_all=c(T17_2_gblup_prediction_all_1_1000,T17_2_gblup_prediction_all_1001_2000,T17_2_gblup_prediction_all_2001_3000,T17_2_gblup_prediction_all_3001_4000,T17_2_gblup_prediction_all_4001_5000,T17_2_gblup_prediction_all_5001_6000,T17_2_gblup_prediction_all_6001_7000,T17_2_gblup_prediction_all_7001_8000,T17_2_gblup_prediction_all_8001_9000,T17_2_gblup_prediction_all_9001_10000,T17_2_gblup_prediction_all_10001_11000,T17_2_gblup_prediction_all_11001_12419)
+
+T17_2_gblup_variances_all_1_1000=readRDS(file="T17_2_gblup_variances_all_1_1000.rds")
+T17_2_gblup_variances_all_1001_2000=readRDS(file="T17_2_gblup_variances_all_1001_2000.rds")
+T17_2_gblup_variances_all_2001_3000=readRDS(file="T17_2_gblup_variances_all_2001_3000.rds")
+T17_2_gblup_variances_all_3001_4000=readRDS(file="T17_2_gblup_variances_all_3001_4000.rds")
+T17_2_gblup_variances_all_4001_5000=readRDS(file="T17_2_gblup_variances_all_4001_5000.rds")
+T17_2_gblup_variances_all_5001_6000=readRDS(file="T17_2_gblup_variances_all_5001_6000.rds")
+T17_2_gblup_variances_all_6001_7000=readRDS(file="T17_2_gblup_variances_all_6001_7000.rds")
+T17_2_gblup_variances_all_7001_8000=readRDS(file="T17_2_gblup_variances_all_7001_8000.rds")
+T17_2_gblup_variances_all_8001_9000=readRDS(file="T17_2_gblup_variances_all_8001_9000.rds")
+T17_2_gblup_variances_all_9001_10000=readRDS(file="T17_2_gblup_variances_all_9001_10000.rds")
+T17_2_gblup_variances_all_10001_11000=readRDS(file="T17_2_gblup_variances_all_10001_11000.rds")
+T17_2_gblup_variances_all_11001_12419=readRDS(file="T17_2_gblup_variances_all_11001_12419.rds")
+T17_2_gblup_variances_all=c(T17_2_gblup_variances_all_1_1000,T17_2_gblup_variances_all_1001_2000,T17_2_gblup_variances_all_2001_3000,T17_2_gblup_variances_all_3001_4000,T17_2_gblup_variances_all_4001_5000,T17_2_gblup_variances_all_5001_6000,T17_2_gblup_variances_all_6001_7000,T17_2_gblup_variances_all_7001_8000,T17_2_gblup_variances_all_8001_9000,T17_2_gblup_variances_all_9001_10000,T17_2_gblup_variances_all_10001_11000,T17_2_gblup_variances_all_11001_12419)
+
+saveRDS(T17_2_gblup_prediction_all,"T17_2_gblup_prediction_all.rds")
+saveRDS(T17_2_gblup_variances_all,"T17_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_2_gfblup_prediction_all_1_1000=readRDS(file="T17_2_gfblup_prediction_all_1_1000.rds")
+T17_2_gfblup_prediction_all_1001_2000=readRDS(file="T17_2_gfblup_prediction_all_1001_2000.rds")
+T17_2_gfblup_prediction_all_2001_3000=readRDS(file="T17_2_gfblup_prediction_all_2001_3000.rds")
+T17_2_gfblup_prediction_all_3001_4000=readRDS(file="T17_2_gfblup_prediction_all_3001_4000.rds")
+T17_2_gfblup_prediction_all_4001_5000=readRDS(file="T17_2_gfblup_prediction_all_4001_5000.rds")
+T17_2_gfblup_prediction_all_5001_6000=readRDS(file="T17_2_gfblup_prediction_all_5001_6000.rds")
+T17_2_gfblup_prediction_all_6001_7000=readRDS(file="T17_2_gfblup_prediction_all_6001_7000.rds")
+T17_2_gfblup_prediction_all_7001_8000=readRDS(file="T17_2_gfblup_prediction_all_7001_8000.rds")
+T17_2_gfblup_prediction_all_8001_9000=readRDS(file="T17_2_gfblup_prediction_all_8001_9000.rds")
+T17_2_gfblup_prediction_all_9001_10000=readRDS(file="T17_2_gfblup_prediction_all_9001_10000.rds")
+T17_2_gfblup_prediction_all_10001_11000=readRDS(file="T17_2_gfblup_prediction_all_10001_11000.rds")
+T17_2_gfblup_prediction_all_11001_12419=readRDS(file="T17_2_gfblup_prediction_all_11001_12419.rds")
+
+T17_2_gfblup_variances_all_1_1000=readRDS(file="T17_2_gfblup_variances_all_1_1000.rds")
+T17_2_gfblup_variances_all_1001_2000=readRDS(file="T17_2_gfblup_variances_all_1001_2000.rds")
+T17_2_gfblup_variances_all_2001_3000=readRDS(file="T17_2_gfblup_variances_all_2001_3000.rds")
+T17_2_gfblup_variances_all_3001_4000=readRDS(file="T17_2_gfblup_variances_all_3001_4000.rds")
+T17_2_gfblup_variances_all_4001_5000=readRDS(file="T17_2_gfblup_variances_all_4001_5000.rds")
+T17_2_gfblup_variances_all_5001_6000=readRDS(file="T17_2_gfblup_variances_all_5001_6000.rds")
+T17_2_gfblup_variances_all_6001_7000=readRDS(file="T17_2_gfblup_variances_all_6001_7000.rds")
+T17_2_gfblup_variances_all_7001_8000=readRDS(file="T17_2_gfblup_variances_all_7001_8000.rds")
+T17_2_gfblup_variances_all_8001_9000=readRDS(file="T17_2_gfblup_variances_all_8001_9000.rds")
+T17_2_gfblup_variances_all_9001_10000=readRDS(file="T17_2_gfblup_variances_all_9001_10000.rds")
+T17_2_gfblup_variances_all_10001_11000=readRDS(file="T17_2_gfblup_variances_all_10001_11000.rds")
+T17_2_gfblup_variances_all_11001_12419=readRDS(file="T17_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T17_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_2_gfblup_variances_all=rep(list(list()),cycles)
+T17_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_1_1000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_1001_2000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_2001_3000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_3001_4000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_4001_5000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_5001_6000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_6001_7000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_7001_8000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_8001_9000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_9001_10000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_10001_11000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_11001_12419[[r]])
+
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_1_1000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_1001_2000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_2001_3000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_3001_4000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_4001_5000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_5001_6000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_6001_7000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_7001_8000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_8001_9000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_9001_10000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_10001_11000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T17_2_gfblup_prediction_all,"T17_2_gfblup_prediction_all.rds")
+saveRDS(T17_2_gfblup_variances_all,"T17_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_3_gblup_prediction_all_1_1000=readRDS(file="T17_3_gblup_prediction_all_1_1000.rds")
+T17_3_gblup_prediction_all_1001_2000=readRDS(file="T17_3_gblup_prediction_all_1001_2000.rds")
+T17_3_gblup_prediction_all_2001_3000=readRDS(file="T17_3_gblup_prediction_all_2001_3000.rds")
+T17_3_gblup_prediction_all_3001_4000=readRDS(file="T17_3_gblup_prediction_all_3001_4000.rds")
+T17_3_gblup_prediction_all_4001_5000=readRDS(file="T17_3_gblup_prediction_all_4001_5000.rds")
+T17_3_gblup_prediction_all_5001_6000=readRDS(file="T17_3_gblup_prediction_all_5001_6000.rds")
+T17_3_gblup_prediction_all_6001_7000=readRDS(file="T17_3_gblup_prediction_all_6001_7000.rds")
+T17_3_gblup_prediction_all_7001_8000=readRDS(file="T17_3_gblup_prediction_all_7001_8000.rds")
+T17_3_gblup_prediction_all_8001_9000=readRDS(file="T17_3_gblup_prediction_all_8001_9000.rds")
+T17_3_gblup_prediction_all_9001_10000=readRDS(file="T17_3_gblup_prediction_all_9001_10000.rds")
+T17_3_gblup_prediction_all_10001_11000=readRDS(file="T17_3_gblup_prediction_all_10001_11000.rds")
+T17_3_gblup_prediction_all_11001_12419=readRDS(file="T17_3_gblup_prediction_all_11001_12419.rds")
+T17_3_gblup_prediction_all=c(T17_3_gblup_prediction_all_1_1000,T17_3_gblup_prediction_all_1001_2000,T17_3_gblup_prediction_all_2001_3000,T17_3_gblup_prediction_all_3001_4000,T17_3_gblup_prediction_all_4001_5000,T17_3_gblup_prediction_all_5001_6000,T17_3_gblup_prediction_all_6001_7000,T17_3_gblup_prediction_all_7001_8000,T17_3_gblup_prediction_all_8001_9000,T17_3_gblup_prediction_all_9001_10000,T17_3_gblup_prediction_all_10001_11000,T17_3_gblup_prediction_all_11001_12419)
+
+T17_3_gblup_variances_all_1_1000=readRDS(file="T17_3_gblup_variances_all_1_1000.rds")
+T17_3_gblup_variances_all_1001_2000=readRDS(file="T17_3_gblup_variances_all_1001_2000.rds")
+T17_3_gblup_variances_all_2001_3000=readRDS(file="T17_3_gblup_variances_all_2001_3000.rds")
+T17_3_gblup_variances_all_3001_4000=readRDS(file="T17_3_gblup_variances_all_3001_4000.rds")
+T17_3_gblup_variances_all_4001_5000=readRDS(file="T17_3_gblup_variances_all_4001_5000.rds")
+T17_3_gblup_variances_all_5001_6000=readRDS(file="T17_3_gblup_variances_all_5001_6000.rds")
+T17_3_gblup_variances_all_6001_7000=readRDS(file="T17_3_gblup_variances_all_6001_7000.rds")
+T17_3_gblup_variances_all_7001_8000=readRDS(file="T17_3_gblup_variances_all_7001_8000.rds")
+T17_3_gblup_variances_all_8001_9000=readRDS(file="T17_3_gblup_variances_all_8001_9000.rds")
+T17_3_gblup_variances_all_9001_10000=readRDS(file="T17_3_gblup_variances_all_9001_10000.rds")
+T17_3_gblup_variances_all_10001_11000=readRDS(file="T17_3_gblup_variances_all_10001_11000.rds")
+T17_3_gblup_variances_all_11001_12419=readRDS(file="T17_3_gblup_variances_all_11001_12419.rds")
+T17_3_gblup_variances_all=c(T17_3_gblup_variances_all_1_1000,T17_3_gblup_variances_all_1001_2000,T17_3_gblup_variances_all_2001_3000,T17_3_gblup_variances_all_3001_4000,T17_3_gblup_variances_all_4001_5000,T17_3_gblup_variances_all_5001_6000,T17_3_gblup_variances_all_6001_7000,T17_3_gblup_variances_all_7001_8000,T17_3_gblup_variances_all_8001_9000,T17_3_gblup_variances_all_9001_10000,T17_3_gblup_variances_all_10001_11000,T17_3_gblup_variances_all_11001_12419)
+
+saveRDS(T17_3_gblup_prediction_all,"T17_3_gblup_prediction_all.rds")
+saveRDS(T17_3_gblup_variances_all,"T17_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_3_gfblup_prediction_all_1_1000=readRDS(file="T17_3_gfblup_prediction_all_1_1000.rds")
+T17_3_gfblup_prediction_all_1001_2000=readRDS(file="T17_3_gfblup_prediction_all_1001_2000.rds")
+T17_3_gfblup_prediction_all_2001_3000=readRDS(file="T17_3_gfblup_prediction_all_2001_3000.rds")
+T17_3_gfblup_prediction_all_3001_4000=readRDS(file="T17_3_gfblup_prediction_all_3001_4000.rds")
+T17_3_gfblup_prediction_all_4001_5000=readRDS(file="T17_3_gfblup_prediction_all_4001_5000.rds")
+T17_3_gfblup_prediction_all_5001_6000=readRDS(file="T17_3_gfblup_prediction_all_5001_6000.rds")
+T17_3_gfblup_prediction_all_6001_7000=readRDS(file="T17_3_gfblup_prediction_all_6001_7000.rds")
+T17_3_gfblup_prediction_all_7001_8000=readRDS(file="T17_3_gfblup_prediction_all_7001_8000.rds")
+T17_3_gfblup_prediction_all_8001_9000=readRDS(file="T17_3_gfblup_prediction_all_8001_9000.rds")
+T17_3_gfblup_prediction_all_9001_10000=readRDS(file="T17_3_gfblup_prediction_all_9001_10000.rds")
+T17_3_gfblup_prediction_all_10001_11000=readRDS(file="T17_3_gfblup_prediction_all_10001_11000.rds")
+T17_3_gfblup_prediction_all_11001_12419=readRDS(file="T17_3_gfblup_prediction_all_11001_12419.rds")
+
+T17_3_gfblup_variances_all_1_1000=readRDS(file="T17_3_gfblup_variances_all_1_1000.rds")
+T17_3_gfblup_variances_all_1001_2000=readRDS(file="T17_3_gfblup_variances_all_1001_2000.rds")
+T17_3_gfblup_variances_all_2001_3000=readRDS(file="T17_3_gfblup_variances_all_2001_3000.rds")
+T17_3_gfblup_variances_all_3001_4000=readRDS(file="T17_3_gfblup_variances_all_3001_4000.rds")
+T17_3_gfblup_variances_all_4001_5000=readRDS(file="T17_3_gfblup_variances_all_4001_5000.rds")
+T17_3_gfblup_variances_all_5001_6000=readRDS(file="T17_3_gfblup_variances_all_5001_6000.rds")
+T17_3_gfblup_variances_all_6001_7000=readRDS(file="T17_3_gfblup_variances_all_6001_7000.rds")
+T17_3_gfblup_variances_all_7001_8000=readRDS(file="T17_3_gfblup_variances_all_7001_8000.rds")
+T17_3_gfblup_variances_all_8001_9000=readRDS(file="T17_3_gfblup_variances_all_8001_9000.rds")
+T17_3_gfblup_variances_all_9001_10000=readRDS(file="T17_3_gfblup_variances_all_9001_10000.rds")
+T17_3_gfblup_variances_all_10001_11000=readRDS(file="T17_3_gfblup_variances_all_10001_11000.rds")
+T17_3_gfblup_variances_all_11001_12419=readRDS(file="T17_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T17_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_3_gfblup_variances_all=rep(list(list()),cycles)
+T17_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_1_1000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_1001_2000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_2001_3000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_3001_4000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_4001_5000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_5001_6000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_6001_7000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_7001_8000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_8001_9000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_9001_10000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_10001_11000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_11001_12419[[r]])
+
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_1_1000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_1001_2000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_2001_3000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_3001_4000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_4001_5000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_5001_6000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_6001_7000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_7001_8000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_8001_9000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_9001_10000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_10001_11000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T17_3_gfblup_prediction_all,"T17_3_gfblup_prediction_all.rds")
+saveRDS(T17_3_gfblup_variances_all,"T17_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_4_gblup_prediction_all_1_1000=readRDS(file="T17_4_gblup_prediction_all_1_1000.rds")
+T17_4_gblup_prediction_all_1001_2000=readRDS(file="T17_4_gblup_prediction_all_1001_2000.rds")
+T17_4_gblup_prediction_all_2001_3000=readRDS(file="T17_4_gblup_prediction_all_2001_3000.rds")
+T17_4_gblup_prediction_all_3001_4000=readRDS(file="T17_4_gblup_prediction_all_3001_4000.rds")
+T17_4_gblup_prediction_all_4001_5000=readRDS(file="T17_4_gblup_prediction_all_4001_5000.rds")
+T17_4_gblup_prediction_all_5001_6000=readRDS(file="T17_4_gblup_prediction_all_5001_6000.rds")
+T17_4_gblup_prediction_all_6001_7000=readRDS(file="T17_4_gblup_prediction_all_6001_7000.rds")
+T17_4_gblup_prediction_all_7001_8000=readRDS(file="T17_4_gblup_prediction_all_7001_8000.rds")
+T17_4_gblup_prediction_all_8001_9000=readRDS(file="T17_4_gblup_prediction_all_8001_9000.rds")
+T17_4_gblup_prediction_all_9001_10000=readRDS(file="T17_4_gblup_prediction_all_9001_10000.rds")
+T17_4_gblup_prediction_all_10001_11000=readRDS(file="T17_4_gblup_prediction_all_10001_11000.rds")
+T17_4_gblup_prediction_all_11001_12419=readRDS(file="T17_4_gblup_prediction_all_11001_12419.rds")
+T17_4_gblup_prediction_all=c(T17_4_gblup_prediction_all_1_1000,T17_4_gblup_prediction_all_1001_2000,T17_4_gblup_prediction_all_2001_3000,T17_4_gblup_prediction_all_3001_4000,T17_4_gblup_prediction_all_4001_5000,T17_4_gblup_prediction_all_5001_6000,T17_4_gblup_prediction_all_6001_7000,T17_4_gblup_prediction_all_7001_8000,T17_4_gblup_prediction_all_8001_9000,T17_4_gblup_prediction_all_9001_10000,T17_4_gblup_prediction_all_10001_11000,T17_4_gblup_prediction_all_11001_12419)
+
+T17_4_gblup_variances_all_1_1000=readRDS(file="T17_4_gblup_variances_all_1_1000.rds")
+T17_4_gblup_variances_all_1001_2000=readRDS(file="T17_4_gblup_variances_all_1001_2000.rds")
+T17_4_gblup_variances_all_2001_3000=readRDS(file="T17_4_gblup_variances_all_2001_3000.rds")
+T17_4_gblup_variances_all_3001_4000=readRDS(file="T17_4_gblup_variances_all_3001_4000.rds")
+T17_4_gblup_variances_all_4001_5000=readRDS(file="T17_4_gblup_variances_all_4001_5000.rds")
+T17_4_gblup_variances_all_5001_6000=readRDS(file="T17_4_gblup_variances_all_5001_6000.rds")
+T17_4_gblup_variances_all_6001_7000=readRDS(file="T17_4_gblup_variances_all_6001_7000.rds")
+T17_4_gblup_variances_all_7001_8000=readRDS(file="T17_4_gblup_variances_all_7001_8000.rds")
+T17_4_gblup_variances_all_8001_9000=readRDS(file="T17_4_gblup_variances_all_8001_9000.rds")
+T17_4_gblup_variances_all_9001_10000=readRDS(file="T17_4_gblup_variances_all_9001_10000.rds")
+T17_4_gblup_variances_all_10001_11000=readRDS(file="T17_4_gblup_variances_all_10001_11000.rds")
+T17_4_gblup_variances_all_11001_12419=readRDS(file="T17_4_gblup_variances_all_11001_12419.rds")
+T17_4_gblup_variances_all=c(T17_4_gblup_variances_all_1_1000,T17_4_gblup_variances_all_1001_2000,T17_4_gblup_variances_all_2001_3000,T17_4_gblup_variances_all_3001_4000,T17_4_gblup_variances_all_4001_5000,T17_4_gblup_variances_all_5001_6000,T17_4_gblup_variances_all_6001_7000,T17_4_gblup_variances_all_7001_8000,T17_4_gblup_variances_all_8001_9000,T17_4_gblup_variances_all_9001_10000,T17_4_gblup_variances_all_10001_11000,T17_4_gblup_variances_all_11001_12419)
+
+saveRDS(T17_4_gblup_prediction_all,"T17_4_gblup_prediction_all.rds")
+saveRDS(T17_4_gblup_variances_all,"T17_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_4_gfblup_prediction_all_1_1000=readRDS(file="T17_4_gfblup_prediction_all_1_1000.rds")
+T17_4_gfblup_prediction_all_1001_2000=readRDS(file="T17_4_gfblup_prediction_all_1001_2000.rds")
+T17_4_gfblup_prediction_all_2001_3000=readRDS(file="T17_4_gfblup_prediction_all_2001_3000.rds")
+T17_4_gfblup_prediction_all_3001_4000=readRDS(file="T17_4_gfblup_prediction_all_3001_4000.rds")
+T17_4_gfblup_prediction_all_4001_5000=readRDS(file="T17_4_gfblup_prediction_all_4001_5000.rds")
+T17_4_gfblup_prediction_all_5001_6000=readRDS(file="T17_4_gfblup_prediction_all_5001_6000.rds")
+T17_4_gfblup_prediction_all_6001_7000=readRDS(file="T17_4_gfblup_prediction_all_6001_7000.rds")
+T17_4_gfblup_prediction_all_7001_8000=readRDS(file="T17_4_gfblup_prediction_all_7001_8000.rds")
+T17_4_gfblup_prediction_all_8001_9000=readRDS(file="T17_4_gfblup_prediction_all_8001_9000.rds")
+T17_4_gfblup_prediction_all_9001_10000=readRDS(file="T17_4_gfblup_prediction_all_9001_10000.rds")
+T17_4_gfblup_prediction_all_10001_11000=readRDS(file="T17_4_gfblup_prediction_all_10001_11000.rds")
+T17_4_gfblup_prediction_all_11001_12419=readRDS(file="T17_4_gfblup_prediction_all_11001_12419.rds")
+
+T17_4_gfblup_variances_all_1_1000=readRDS(file="T17_4_gfblup_variances_all_1_1000.rds")
+T17_4_gfblup_variances_all_1001_2000=readRDS(file="T17_4_gfblup_variances_all_1001_2000.rds")
+T17_4_gfblup_variances_all_2001_3000=readRDS(file="T17_4_gfblup_variances_all_2001_3000.rds")
+T17_4_gfblup_variances_all_3001_4000=readRDS(file="T17_4_gfblup_variances_all_3001_4000.rds")
+T17_4_gfblup_variances_all_4001_5000=readRDS(file="T17_4_gfblup_variances_all_4001_5000.rds")
+T17_4_gfblup_variances_all_5001_6000=readRDS(file="T17_4_gfblup_variances_all_5001_6000.rds")
+T17_4_gfblup_variances_all_6001_7000=readRDS(file="T17_4_gfblup_variances_all_6001_7000.rds")
+T17_4_gfblup_variances_all_7001_8000=readRDS(file="T17_4_gfblup_variances_all_7001_8000.rds")
+T17_4_gfblup_variances_all_8001_9000=readRDS(file="T17_4_gfblup_variances_all_8001_9000.rds")
+T17_4_gfblup_variances_all_9001_10000=readRDS(file="T17_4_gfblup_variances_all_9001_10000.rds")
+T17_4_gfblup_variances_all_10001_11000=readRDS(file="T17_4_gfblup_variances_all_10001_11000.rds")
+T17_4_gfblup_variances_all_11001_12419=readRDS(file="T17_4_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T17_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_4_gfblup_variances_all=rep(list(list()),cycles)
+T17_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_1_1000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_1001_2000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_2001_3000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_3001_4000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_4001_5000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_5001_6000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_6001_7000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_7001_8000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_8001_9000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_9001_10000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_10001_11000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_11001_12419[[r]])
+
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_1_1000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_1001_2000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_2001_3000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_3001_4000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_4001_5000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_5001_6000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_6001_7000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_7001_8000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_8001_9000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_9001_10000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_10001_11000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T17_4_gfblup_prediction_all,"T17_4_gfblup_prediction_all.rds")
+saveRDS(T17_4_gfblup_variances_all,"T17_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_5_gblup_prediction_all_1_1000=readRDS(file="T17_5_gblup_prediction_all_1_1000.rds")
+T17_5_gblup_prediction_all_1001_2000=readRDS(file="T17_5_gblup_prediction_all_1001_2000.rds")
+T17_5_gblup_prediction_all_2001_3000=readRDS(file="T17_5_gblup_prediction_all_2001_3000.rds")
+T17_5_gblup_prediction_all_3001_4000=readRDS(file="T17_5_gblup_prediction_all_3001_4000.rds")
+T17_5_gblup_prediction_all_4001_5000=readRDS(file="T17_5_gblup_prediction_all_4001_5000.rds")
+T17_5_gblup_prediction_all_5001_6000=readRDS(file="T17_5_gblup_prediction_all_5001_6000.rds")
+T17_5_gblup_prediction_all_6001_7000=readRDS(file="T17_5_gblup_prediction_all_6001_7000.rds")
+T17_5_gblup_prediction_all_7001_8000=readRDS(file="T17_5_gblup_prediction_all_7001_8000.rds")
+T17_5_gblup_prediction_all_8001_9000=readRDS(file="T17_5_gblup_prediction_all_8001_9000.rds")
+T17_5_gblup_prediction_all_9001_10000=readRDS(file="T17_5_gblup_prediction_all_9001_10000.rds")
+T17_5_gblup_prediction_all_10001_11000=readRDS(file="T17_5_gblup_prediction_all_10001_11000.rds")
+T17_5_gblup_prediction_all_11001_12419=readRDS(file="T17_5_gblup_prediction_all_11001_12419.rds")
+T17_5_gblup_prediction_all=c(T17_5_gblup_prediction_all_1_1000,T17_5_gblup_prediction_all_1001_2000,T17_5_gblup_prediction_all_2001_3000,T17_5_gblup_prediction_all_3001_4000,T17_5_gblup_prediction_all_4001_5000,T17_5_gblup_prediction_all_5001_6000,T17_5_gblup_prediction_all_6001_7000,T17_5_gblup_prediction_all_7001_8000,T17_5_gblup_prediction_all_8001_9000,T17_5_gblup_prediction_all_9001_10000,T17_5_gblup_prediction_all_10001_11000,T17_5_gblup_prediction_all_11001_12419)
+
+T17_5_gblup_variances_all_1_1000=readRDS(file="T17_5_gblup_variances_all_1_1000.rds")
+T17_5_gblup_variances_all_1001_2000=readRDS(file="T17_5_gblup_variances_all_1001_2000.rds")
+T17_5_gblup_variances_all_2001_3000=readRDS(file="T17_5_gblup_variances_all_2001_3000.rds")
+T17_5_gblup_variances_all_3001_4000=readRDS(file="T17_5_gblup_variances_all_3001_4000.rds")
+T17_5_gblup_variances_all_4001_5000=readRDS(file="T17_5_gblup_variances_all_4001_5000.rds")
+T17_5_gblup_variances_all_5001_6000=readRDS(file="T17_5_gblup_variances_all_5001_6000.rds")
+T17_5_gblup_variances_all_6001_7000=readRDS(file="T17_5_gblup_variances_all_6001_7000.rds")
+T17_5_gblup_variances_all_7001_8000=readRDS(file="T17_5_gblup_variances_all_7001_8000.rds")
+T17_5_gblup_variances_all_8001_9000=readRDS(file="T17_5_gblup_variances_all_8001_9000.rds")
+T17_5_gblup_variances_all_9001_10000=readRDS(file="T17_5_gblup_variances_all_9001_10000.rds")
+T17_5_gblup_variances_all_10001_11000=readRDS(file="T17_5_gblup_variances_all_10001_11000.rds")
+T17_5_gblup_variances_all_11001_12419=readRDS(file="T17_5_gblup_variances_all_11001_12419.rds")
+T17_5_gblup_variances_all=c(T17_5_gblup_variances_all_1_1000,T17_5_gblup_variances_all_1001_2000,T17_5_gblup_variances_all_2001_3000,T17_5_gblup_variances_all_3001_4000,T17_5_gblup_variances_all_4001_5000,T17_5_gblup_variances_all_5001_6000,T17_5_gblup_variances_all_6001_7000,T17_5_gblup_variances_all_7001_8000,T17_5_gblup_variances_all_8001_9000,T17_5_gblup_variances_all_9001_10000,T17_5_gblup_variances_all_10001_11000,T17_5_gblup_variances_all_11001_12419)
+
+saveRDS(T17_5_gblup_prediction_all,"T17_5_gblup_prediction_all.rds")
+saveRDS(T17_5_gblup_variances_all,"T17_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_5_gfblup_prediction_all_1_1000=readRDS(file="T17_5_gfblup_prediction_all_1_1000.rds")
+T17_5_gfblup_prediction_all_1001_2000=readRDS(file="T17_5_gfblup_prediction_all_1001_2000.rds")
+T17_5_gfblup_prediction_all_2001_3000=readRDS(file="T17_5_gfblup_prediction_all_2001_3000.rds")
+T17_5_gfblup_prediction_all_3001_4000=readRDS(file="T17_5_gfblup_prediction_all_3001_4000.rds")
+T17_5_gfblup_prediction_all_4001_5000=readRDS(file="T17_5_gfblup_prediction_all_4001_5000.rds")
+T17_5_gfblup_prediction_all_5001_6000=readRDS(file="T17_5_gfblup_prediction_all_5001_6000.rds")
+T17_5_gfblup_prediction_all_6001_7000=readRDS(file="T17_5_gfblup_prediction_all_6001_7000.rds")
+T17_5_gfblup_prediction_all_7001_8000=readRDS(file="T17_5_gfblup_prediction_all_7001_8000.rds")
+T17_5_gfblup_prediction_all_8001_9000=readRDS(file="T17_5_gfblup_prediction_all_8001_9000.rds")
+T17_5_gfblup_prediction_all_9001_10000=readRDS(file="T17_5_gfblup_prediction_all_9001_10000.rds")
+T17_5_gfblup_prediction_all_10001_11000=readRDS(file="T17_5_gfblup_prediction_all_10001_11000.rds")
+T17_5_gfblup_prediction_all_11001_12419=readRDS(file="T17_5_gfblup_prediction_all_11001_12419.rds")
+
+T17_5_gfblup_variances_all_1_1000=readRDS(file="T17_5_gfblup_variances_all_1_1000.rds")
+T17_5_gfblup_variances_all_1001_2000=readRDS(file="T17_5_gfblup_variances_all_1001_2000.rds")
+T17_5_gfblup_variances_all_2001_3000=readRDS(file="T17_5_gfblup_variances_all_2001_3000.rds")
+T17_5_gfblup_variances_all_3001_4000=readRDS(file="T17_5_gfblup_variances_all_3001_4000.rds")
+T17_5_gfblup_variances_all_4001_5000=readRDS(file="T17_5_gfblup_variances_all_4001_5000.rds")
+T17_5_gfblup_variances_all_5001_6000=readRDS(file="T17_5_gfblup_variances_all_5001_6000.rds")
+T17_5_gfblup_variances_all_6001_7000=readRDS(file="T17_5_gfblup_variances_all_6001_7000.rds")
+T17_5_gfblup_variances_all_7001_8000=readRDS(file="T17_5_gfblup_variances_all_7001_8000.rds")
+T17_5_gfblup_variances_all_8001_9000=readRDS(file="T17_5_gfblup_variances_all_8001_9000.rds")
+T17_5_gfblup_variances_all_9001_10000=readRDS(file="T17_5_gfblup_variances_all_9001_10000.rds")
+T17_5_gfblup_variances_all_10001_11000=readRDS(file="T17_5_gfblup_variances_all_10001_11000.rds")
+T17_5_gfblup_variances_all_11001_12419=readRDS(file="T17_5_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T17_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_5_gfblup_variances_all=rep(list(list()),cycles)
+T17_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_1_1000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_1001_2000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_2001_3000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_3001_4000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_4001_5000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_5001_6000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_6001_7000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_7001_8000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_8001_9000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_9001_10000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_10001_11000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_11001_12419[[r]])
+
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_1_1000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_1001_2000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_2001_3000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_3001_4000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_4001_5000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_5001_6000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_6001_7000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_7001_8000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_8001_9000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_9001_10000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_10001_11000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T17_5_gfblup_prediction_all,"T17_5_gfblup_prediction_all.rds")
+saveRDS(T17_5_gfblup_variances_all,"T17_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_6_gblup_prediction_all_1_1000=readRDS(file="T17_6_gblup_prediction_all_1_1000.rds")
+T17_6_gblup_prediction_all_1001_2000=readRDS(file="T17_6_gblup_prediction_all_1001_2000.rds")
+T17_6_gblup_prediction_all_2001_3000=readRDS(file="T17_6_gblup_prediction_all_2001_3000.rds")
+T17_6_gblup_prediction_all_3001_4000=readRDS(file="T17_6_gblup_prediction_all_3001_4000.rds")
+T17_6_gblup_prediction_all_4001_5000=readRDS(file="T17_6_gblup_prediction_all_4001_5000.rds")
+T17_6_gblup_prediction_all_5001_6000=readRDS(file="T17_6_gblup_prediction_all_5001_6000.rds")
+T17_6_gblup_prediction_all_6001_7000=readRDS(file="T17_6_gblup_prediction_all_6001_7000.rds")
+T17_6_gblup_prediction_all_7001_8000=readRDS(file="T17_6_gblup_prediction_all_7001_8000.rds")
+T17_6_gblup_prediction_all_8001_9000=readRDS(file="T17_6_gblup_prediction_all_8001_9000.rds")
+T17_6_gblup_prediction_all_9001_10000=readRDS(file="T17_6_gblup_prediction_all_9001_10000.rds")
+T17_6_gblup_prediction_all_10001_11000=readRDS(file="T17_6_gblup_prediction_all_10001_11000.rds")
+T17_6_gblup_prediction_all_11001_12419=readRDS(file="T17_6_gblup_prediction_all_11001_12419.rds")
+T17_6_gblup_prediction_all=c(T17_6_gblup_prediction_all_1_1000,T17_6_gblup_prediction_all_1001_2000,T17_6_gblup_prediction_all_2001_3000,T17_6_gblup_prediction_all_3001_4000,T17_6_gblup_prediction_all_4001_5000,T17_6_gblup_prediction_all_5001_6000,T17_6_gblup_prediction_all_6001_7000,T17_6_gblup_prediction_all_7001_8000,T17_6_gblup_prediction_all_8001_9000,T17_6_gblup_prediction_all_9001_10000,T17_6_gblup_prediction_all_10001_11000,T17_6_gblup_prediction_all_11001_12419)
+
+T17_6_gblup_variances_all_1_1000=readRDS(file="T17_6_gblup_variances_all_1_1000.rds")
+T17_6_gblup_variances_all_1001_2000=readRDS(file="T17_6_gblup_variances_all_1001_2000.rds")
+T17_6_gblup_variances_all_2001_3000=readRDS(file="T17_6_gblup_variances_all_2001_3000.rds")
+T17_6_gblup_variances_all_3001_4000=readRDS(file="T17_6_gblup_variances_all_3001_4000.rds")
+T17_6_gblup_variances_all_4001_5000=readRDS(file="T17_6_gblup_variances_all_4001_5000.rds")
+T17_6_gblup_variances_all_5001_6000=readRDS(file="T17_6_gblup_variances_all_5001_6000.rds")
+T17_6_gblup_variances_all_6001_7000=readRDS(file="T17_6_gblup_variances_all_6001_7000.rds")
+T17_6_gblup_variances_all_7001_8000=readRDS(file="T17_6_gblup_variances_all_7001_8000.rds")
+T17_6_gblup_variances_all_8001_9000=readRDS(file="T17_6_gblup_variances_all_8001_9000.rds")
+T17_6_gblup_variances_all_9001_10000=readRDS(file="T17_6_gblup_variances_all_9001_10000.rds")
+T17_6_gblup_variances_all_10001_11000=readRDS(file="T17_6_gblup_variances_all_10001_11000.rds")
+T17_6_gblup_variances_all_11001_12419=readRDS(file="T17_6_gblup_variances_all_11001_12419.rds")
+T17_6_gblup_variances_all=c(T17_6_gblup_variances_all_1_1000,T17_6_gblup_variances_all_1001_2000,T17_6_gblup_variances_all_2001_3000,T17_6_gblup_variances_all_3001_4000,T17_6_gblup_variances_all_4001_5000,T17_6_gblup_variances_all_5001_6000,T17_6_gblup_variances_all_6001_7000,T17_6_gblup_variances_all_7001_8000,T17_6_gblup_variances_all_8001_9000,T17_6_gblup_variances_all_9001_10000,T17_6_gblup_variances_all_10001_11000,T17_6_gblup_variances_all_11001_12419)
+
+saveRDS(T17_6_gblup_prediction_all,"T17_6_gblup_prediction_all.rds")
+saveRDS(T17_6_gblup_variances_all,"T17_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_6_gfblup_prediction_all_1_1000=readRDS(file="T17_6_gfblup_prediction_all_1_1000.rds")
+T17_6_gfblup_prediction_all_1001_2000=readRDS(file="T17_6_gfblup_prediction_all_1001_2000.rds")
+T17_6_gfblup_prediction_all_2001_3000=readRDS(file="T17_6_gfblup_prediction_all_2001_3000.rds")
+T17_6_gfblup_prediction_all_3001_4000=readRDS(file="T17_6_gfblup_prediction_all_3001_4000.rds")
+T17_6_gfblup_prediction_all_4001_5000=readRDS(file="T17_6_gfblup_prediction_all_4001_5000.rds")
+T17_6_gfblup_prediction_all_5001_6000=readRDS(file="T17_6_gfblup_prediction_all_5001_6000.rds")
+T17_6_gfblup_prediction_all_6001_7000=readRDS(file="T17_6_gfblup_prediction_all_6001_7000.rds")
+T17_6_gfblup_prediction_all_7001_8000=readRDS(file="T17_6_gfblup_prediction_all_7001_8000.rds")
+T17_6_gfblup_prediction_all_8001_9000=readRDS(file="T17_6_gfblup_prediction_all_8001_9000.rds")
+T17_6_gfblup_prediction_all_9001_10000=readRDS(file="T17_6_gfblup_prediction_all_9001_10000.rds")
+T17_6_gfblup_prediction_all_10001_11000=readRDS(file="T17_6_gfblup_prediction_all_10001_11000.rds")
+T17_6_gfblup_prediction_all_11001_12419=readRDS(file="T17_6_gfblup_prediction_all_11001_12419.rds")
+
+T17_6_gfblup_variances_all_1_1000=readRDS(file="T17_6_gfblup_variances_all_1_1000.rds")
+T17_6_gfblup_variances_all_1001_2000=readRDS(file="T17_6_gfblup_variances_all_1001_2000.rds")
+T17_6_gfblup_variances_all_2001_3000=readRDS(file="T17_6_gfblup_variances_all_2001_3000.rds")
+T17_6_gfblup_variances_all_3001_4000=readRDS(file="T17_6_gfblup_variances_all_3001_4000.rds")
+T17_6_gfblup_variances_all_4001_5000=readRDS(file="T17_6_gfblup_variances_all_4001_5000.rds")
+T17_6_gfblup_variances_all_5001_6000=readRDS(file="T17_6_gfblup_variances_all_5001_6000.rds")
+T17_6_gfblup_variances_all_6001_7000=readRDS(file="T17_6_gfblup_variances_all_6001_7000.rds")
+T17_6_gfblup_variances_all_7001_8000=readRDS(file="T17_6_gfblup_variances_all_7001_8000.rds")
+T17_6_gfblup_variances_all_8001_9000=readRDS(file="T17_6_gfblup_variances_all_8001_9000.rds")
+T17_6_gfblup_variances_all_9001_10000=readRDS(file="T17_6_gfblup_variances_all_9001_10000.rds")
+T17_6_gfblup_variances_all_10001_11000=readRDS(file="T17_6_gfblup_variances_all_10001_11000.rds")
+T17_6_gfblup_variances_all_11001_12419=readRDS(file="T17_6_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T17_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_6_gfblup_variances_all=rep(list(list()),cycles)
+T17_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_1_1000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_1001_2000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_2001_3000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_3001_4000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_4001_5000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_5001_6000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_6001_7000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_7001_8000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_8001_9000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_9001_10000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_10001_11000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_11001_12419[[r]])
+
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_1_1000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_1001_2000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_2001_3000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_3001_4000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_4001_5000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_5001_6000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_6001_7000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_7001_8000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_8001_9000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_9001_10000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_10001_11000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T17_6_gfblup_prediction_all,"T17_6_gfblup_prediction_all.rds")
+saveRDS(T17_6_gfblup_variances_all,"T17_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_7_gblup_prediction_all_1_1000=readRDS(file="T17_7_gblup_prediction_all_1_1000.rds")
+T17_7_gblup_prediction_all_1001_2000=readRDS(file="T17_7_gblup_prediction_all_1001_2000.rds")
+T17_7_gblup_prediction_all_2001_3000=readRDS(file="T17_7_gblup_prediction_all_2001_3000.rds")
+T17_7_gblup_prediction_all_3001_4000=readRDS(file="T17_7_gblup_prediction_all_3001_4000.rds")
+T17_7_gblup_prediction_all_4001_5000=readRDS(file="T17_7_gblup_prediction_all_4001_5000.rds")
+T17_7_gblup_prediction_all_5001_6000=readRDS(file="T17_7_gblup_prediction_all_5001_6000.rds")
+T17_7_gblup_prediction_all_6001_7000=readRDS(file="T17_7_gblup_prediction_all_6001_7000.rds")
+T17_7_gblup_prediction_all_7001_8000=readRDS(file="T17_7_gblup_prediction_all_7001_8000.rds")
+T17_7_gblup_prediction_all_8001_9000=readRDS(file="T17_7_gblup_prediction_all_8001_9000.rds")
+T17_7_gblup_prediction_all_9001_10000=readRDS(file="T17_7_gblup_prediction_all_9001_10000.rds")
+T17_7_gblup_prediction_all_10001_11000=readRDS(file="T17_7_gblup_prediction_all_10001_11000.rds")
+T17_7_gblup_prediction_all_11001_12419=readRDS(file="T17_7_gblup_prediction_all_11001_12419.rds")
+T17_7_gblup_prediction_all=c(T17_7_gblup_prediction_all_1_1000,T17_7_gblup_prediction_all_1001_2000,T17_7_gblup_prediction_all_2001_3000,T17_7_gblup_prediction_all_3001_4000,T17_7_gblup_prediction_all_4001_5000,T17_7_gblup_prediction_all_5001_6000,T17_7_gblup_prediction_all_6001_7000,T17_7_gblup_prediction_all_7001_8000,T17_7_gblup_prediction_all_8001_9000,T17_7_gblup_prediction_all_9001_10000,T17_7_gblup_prediction_all_10001_11000,T17_7_gblup_prediction_all_11001_12419)
+
+T17_7_gblup_variances_all_1_1000=readRDS(file="T17_7_gblup_variances_all_1_1000.rds")
+T17_7_gblup_variances_all_1001_2000=readRDS(file="T17_7_gblup_variances_all_1001_2000.rds")
+T17_7_gblup_variances_all_2001_3000=readRDS(file="T17_7_gblup_variances_all_2001_3000.rds")
+T17_7_gblup_variances_all_3001_4000=readRDS(file="T17_7_gblup_variances_all_3001_4000.rds")
+T17_7_gblup_variances_all_4001_5000=readRDS(file="T17_7_gblup_variances_all_4001_5000.rds")
+T17_7_gblup_variances_all_5001_6000=readRDS(file="T17_7_gblup_variances_all_5001_6000.rds")
+T17_7_gblup_variances_all_6001_7000=readRDS(file="T17_7_gblup_variances_all_6001_7000.rds")
+T17_7_gblup_variances_all_7001_8000=readRDS(file="T17_7_gblup_variances_all_7001_8000.rds")
+T17_7_gblup_variances_all_8001_9000=readRDS(file="T17_7_gblup_variances_all_8001_9000.rds")
+T17_7_gblup_variances_all_9001_10000=readRDS(file="T17_7_gblup_variances_all_9001_10000.rds")
+T17_7_gblup_variances_all_10001_11000=readRDS(file="T17_7_gblup_variances_all_10001_11000.rds")
+T17_7_gblup_variances_all_11001_12419=readRDS(file="T17_7_gblup_variances_all_11001_12419.rds")
+T17_7_gblup_variances_all=c(T17_7_gblup_variances_all_1_1000,T17_7_gblup_variances_all_1001_2000,T17_7_gblup_variances_all_2001_3000,T17_7_gblup_variances_all_3001_4000,T17_7_gblup_variances_all_4001_5000,T17_7_gblup_variances_all_5001_6000,T17_7_gblup_variances_all_6001_7000,T17_7_gblup_variances_all_7001_8000,T17_7_gblup_variances_all_8001_9000,T17_7_gblup_variances_all_9001_10000,T17_7_gblup_variances_all_10001_11000,T17_7_gblup_variances_all_11001_12419)
+
+saveRDS(T17_7_gblup_prediction_all,"T17_7_gblup_prediction_all.rds")
+saveRDS(T17_7_gblup_variances_all,"T17_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_7_gfblup_prediction_all_1_1000=readRDS(file="T17_7_gfblup_prediction_all_1_1000.rds")
+T17_7_gfblup_prediction_all_1001_2000=readRDS(file="T17_7_gfblup_prediction_all_1001_2000.rds")
+T17_7_gfblup_prediction_all_2001_3000=readRDS(file="T17_7_gfblup_prediction_all_2001_3000.rds")
+T17_7_gfblup_prediction_all_3001_4000=readRDS(file="T17_7_gfblup_prediction_all_3001_4000.rds")
+T17_7_gfblup_prediction_all_4001_5000=readRDS(file="T17_7_gfblup_prediction_all_4001_5000.rds")
+T17_7_gfblup_prediction_all_5001_6000=readRDS(file="T17_7_gfblup_prediction_all_5001_6000.rds")
+T17_7_gfblup_prediction_all_6001_7000=readRDS(file="T17_7_gfblup_prediction_all_6001_7000.rds")
+T17_7_gfblup_prediction_all_7001_8000=readRDS(file="T17_7_gfblup_prediction_all_7001_8000.rds")
+T17_7_gfblup_prediction_all_8001_9000=readRDS(file="T17_7_gfblup_prediction_all_8001_9000.rds")
+T17_7_gfblup_prediction_all_9001_10000=readRDS(file="T17_7_gfblup_prediction_all_9001_10000.rds")
+T17_7_gfblup_prediction_all_10001_11000=readRDS(file="T17_7_gfblup_prediction_all_10001_11000.rds")
+T17_7_gfblup_prediction_all_11001_12419=readRDS(file="T17_7_gfblup_prediction_all_11001_12419.rds")
+
+T17_7_gfblup_variances_all_1_1000=readRDS(file="T17_7_gfblup_variances_all_1_1000.rds")
+T17_7_gfblup_variances_all_1001_2000=readRDS(file="T17_7_gfblup_variances_all_1001_2000.rds")
+T17_7_gfblup_variances_all_2001_3000=readRDS(file="T17_7_gfblup_variances_all_2001_3000.rds")
+T17_7_gfblup_variances_all_3001_4000=readRDS(file="T17_7_gfblup_variances_all_3001_4000.rds")
+T17_7_gfblup_variances_all_4001_5000=readRDS(file="T17_7_gfblup_variances_all_4001_5000.rds")
+T17_7_gfblup_variances_all_5001_6000=readRDS(file="T17_7_gfblup_variances_all_5001_6000.rds")
+T17_7_gfblup_variances_all_6001_7000=readRDS(file="T17_7_gfblup_variances_all_6001_7000.rds")
+T17_7_gfblup_variances_all_7001_8000=readRDS(file="T17_7_gfblup_variances_all_7001_8000.rds")
+T17_7_gfblup_variances_all_8001_9000=readRDS(file="T17_7_gfblup_variances_all_8001_9000.rds")
+T17_7_gfblup_variances_all_9001_10000=readRDS(file="T17_7_gfblup_variances_all_9001_10000.rds")
+T17_7_gfblup_variances_all_10001_11000=readRDS(file="T17_7_gfblup_variances_all_10001_11000.rds")
+T17_7_gfblup_variances_all_11001_12419=readRDS(file="T17_7_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T17_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_7_gfblup_variances_all=rep(list(list()),cycles)
+T17_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_1_1000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_1001_2000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_2001_3000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_3001_4000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_4001_5000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_5001_6000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_6001_7000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_7001_8000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_8001_9000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_9001_10000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_10001_11000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_11001_12419[[r]])
+
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_1_1000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_1001_2000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_2001_3000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_3001_4000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_4001_5000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_5001_6000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_6001_7000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_7001_8000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_8001_9000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_9001_10000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_10001_11000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T17_7_gfblup_prediction_all,"T17_7_gfblup_prediction_all.rds")
+saveRDS(T17_7_gfblup_variances_all,"T17_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_8_gblup_prediction_all_1_1000=readRDS(file="T17_8_gblup_prediction_all_1_1000.rds")
+T17_8_gblup_prediction_all_1001_2000=readRDS(file="T17_8_gblup_prediction_all_1001_2000.rds")
+T17_8_gblup_prediction_all_2001_3000=readRDS(file="T17_8_gblup_prediction_all_2001_3000.rds")
+T17_8_gblup_prediction_all_3001_4000=readRDS(file="T17_8_gblup_prediction_all_3001_4000.rds")
+T17_8_gblup_prediction_all_4001_5000=readRDS(file="T17_8_gblup_prediction_all_4001_5000.rds")
+T17_8_gblup_prediction_all_5001_6000=readRDS(file="T17_8_gblup_prediction_all_5001_6000.rds")
+T17_8_gblup_prediction_all_6001_7000=readRDS(file="T17_8_gblup_prediction_all_6001_7000.rds")
+T17_8_gblup_prediction_all_7001_8000=readRDS(file="T17_8_gblup_prediction_all_7001_8000.rds")
+T17_8_gblup_prediction_all_8001_9000=readRDS(file="T17_8_gblup_prediction_all_8001_9000.rds")
+T17_8_gblup_prediction_all_9001_10000=readRDS(file="T17_8_gblup_prediction_all_9001_10000.rds")
+T17_8_gblup_prediction_all_10001_11000=readRDS(file="T17_8_gblup_prediction_all_10001_11000.rds")
+T17_8_gblup_prediction_all_11001_12419=readRDS(file="T17_8_gblup_prediction_all_11001_12419.rds")
+T17_8_gblup_prediction_all=c(T17_8_gblup_prediction_all_1_1000,T17_8_gblup_prediction_all_1001_2000,T17_8_gblup_prediction_all_2001_3000,T17_8_gblup_prediction_all_3001_4000,T17_8_gblup_prediction_all_4001_5000,T17_8_gblup_prediction_all_5001_6000,T17_8_gblup_prediction_all_6001_7000,T17_8_gblup_prediction_all_7001_8000,T17_8_gblup_prediction_all_8001_9000,T17_8_gblup_prediction_all_9001_10000,T17_8_gblup_prediction_all_10001_11000,T17_8_gblup_prediction_all_11001_12419)
+
+T17_8_gblup_variances_all_1_1000=readRDS(file="T17_8_gblup_variances_all_1_1000.rds")
+T17_8_gblup_variances_all_1001_2000=readRDS(file="T17_8_gblup_variances_all_1001_2000.rds")
+T17_8_gblup_variances_all_2001_3000=readRDS(file="T17_8_gblup_variances_all_2001_3000.rds")
+T17_8_gblup_variances_all_3001_4000=readRDS(file="T17_8_gblup_variances_all_3001_4000.rds")
+T17_8_gblup_variances_all_4001_5000=readRDS(file="T17_8_gblup_variances_all_4001_5000.rds")
+T17_8_gblup_variances_all_5001_6000=readRDS(file="T17_8_gblup_variances_all_5001_6000.rds")
+T17_8_gblup_variances_all_6001_7000=readRDS(file="T17_8_gblup_variances_all_6001_7000.rds")
+T17_8_gblup_variances_all_7001_8000=readRDS(file="T17_8_gblup_variances_all_7001_8000.rds")
+T17_8_gblup_variances_all_8001_9000=readRDS(file="T17_8_gblup_variances_all_8001_9000.rds")
+T17_8_gblup_variances_all_9001_10000=readRDS(file="T17_8_gblup_variances_all_9001_10000.rds")
+T17_8_gblup_variances_all_10001_11000=readRDS(file="T17_8_gblup_variances_all_10001_11000.rds")
+T17_8_gblup_variances_all_11001_12419=readRDS(file="T17_8_gblup_variances_all_11001_12419.rds")
+T17_8_gblup_variances_all=c(T17_8_gblup_variances_all_1_1000,T17_8_gblup_variances_all_1001_2000,T17_8_gblup_variances_all_2001_3000,T17_8_gblup_variances_all_3001_4000,T17_8_gblup_variances_all_4001_5000,T17_8_gblup_variances_all_5001_6000,T17_8_gblup_variances_all_6001_7000,T17_8_gblup_variances_all_7001_8000,T17_8_gblup_variances_all_8001_9000,T17_8_gblup_variances_all_9001_10000,T17_8_gblup_variances_all_10001_11000,T17_8_gblup_variances_all_11001_12419)
+
+saveRDS(T17_8_gblup_prediction_all,"T17_8_gblup_prediction_all.rds")
+saveRDS(T17_8_gblup_variances_all,"T17_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_8_gfblup_prediction_all_1_1000=readRDS(file="T17_8_gfblup_prediction_all_1_1000.rds")
+T17_8_gfblup_prediction_all_1001_2000=readRDS(file="T17_8_gfblup_prediction_all_1001_2000.rds")
+T17_8_gfblup_prediction_all_2001_3000=readRDS(file="T17_8_gfblup_prediction_all_2001_3000.rds")
+T17_8_gfblup_prediction_all_3001_4000=readRDS(file="T17_8_gfblup_prediction_all_3001_4000.rds")
+T17_8_gfblup_prediction_all_4001_5000=readRDS(file="T17_8_gfblup_prediction_all_4001_5000.rds")
+T17_8_gfblup_prediction_all_5001_6000=readRDS(file="T17_8_gfblup_prediction_all_5001_6000.rds")
+T17_8_gfblup_prediction_all_6001_7000=readRDS(file="T17_8_gfblup_prediction_all_6001_7000.rds")
+T17_8_gfblup_prediction_all_7001_8000=readRDS(file="T17_8_gfblup_prediction_all_7001_8000.rds")
+T17_8_gfblup_prediction_all_8001_9000=readRDS(file="T17_8_gfblup_prediction_all_8001_9000.rds")
+T17_8_gfblup_prediction_all_9001_10000=readRDS(file="T17_8_gfblup_prediction_all_9001_10000.rds")
+T17_8_gfblup_prediction_all_10001_11000=readRDS(file="T17_8_gfblup_prediction_all_10001_11000.rds")
+T17_8_gfblup_prediction_all_11001_12419=readRDS(file="T17_8_gfblup_prediction_all_11001_12419.rds")
+
+T17_8_gfblup_variances_all_1_1000=readRDS(file="T17_8_gfblup_variances_all_1_1000.rds")
+T17_8_gfblup_variances_all_1001_2000=readRDS(file="T17_8_gfblup_variances_all_1001_2000.rds")
+T17_8_gfblup_variances_all_2001_3000=readRDS(file="T17_8_gfblup_variances_all_2001_3000.rds")
+T17_8_gfblup_variances_all_3001_4000=readRDS(file="T17_8_gfblup_variances_all_3001_4000.rds")
+T17_8_gfblup_variances_all_4001_5000=readRDS(file="T17_8_gfblup_variances_all_4001_5000.rds")
+T17_8_gfblup_variances_all_5001_6000=readRDS(file="T17_8_gfblup_variances_all_5001_6000.rds")
+T17_8_gfblup_variances_all_6001_7000=readRDS(file="T17_8_gfblup_variances_all_6001_7000.rds")
+T17_8_gfblup_variances_all_7001_8000=readRDS(file="T17_8_gfblup_variances_all_7001_8000.rds")
+T17_8_gfblup_variances_all_8001_9000=readRDS(file="T17_8_gfblup_variances_all_8001_9000.rds")
+T17_8_gfblup_variances_all_9001_10000=readRDS(file="T17_8_gfblup_variances_all_9001_10000.rds")
+T17_8_gfblup_variances_all_10001_11000=readRDS(file="T17_8_gfblup_variances_all_10001_11000.rds")
+T17_8_gfblup_variances_all_11001_12419=readRDS(file="T17_8_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T17_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_8_gfblup_variances_all=rep(list(list()),cycles)
+T17_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_1_1000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_1001_2000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_2001_3000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_3001_4000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_4001_5000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_5001_6000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_6001_7000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_7001_8000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_8001_9000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_9001_10000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_10001_11000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_11001_12419[[r]])
+
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_1_1000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_1001_2000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_2001_3000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_3001_4000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_4001_5000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_5001_6000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_6001_7000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_7001_8000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_8001_9000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_9001_10000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_10001_11000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T17_8_gfblup_prediction_all,"T17_8_gfblup_prediction_all.rds")
+saveRDS(T17_8_gfblup_variances_all,"T17_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_1_gblup_prediction_all_1_1000=readRDS(file="T18_1_gblup_prediction_all_1_1000.rds")
+T18_1_gblup_prediction_all_1001_2000=readRDS(file="T18_1_gblup_prediction_all_1001_2000.rds")
+T18_1_gblup_prediction_all_2001_3000=readRDS(file="T18_1_gblup_prediction_all_2001_3000.rds")
+T18_1_gblup_prediction_all_3001_4000=readRDS(file="T18_1_gblup_prediction_all_3001_4000.rds")
+T18_1_gblup_prediction_all_4001_5000=readRDS(file="T18_1_gblup_prediction_all_4001_5000.rds")
+T18_1_gblup_prediction_all_5001_6000=readRDS(file="T18_1_gblup_prediction_all_5001_6000.rds")
+T18_1_gblup_prediction_all_6001_7000=readRDS(file="T18_1_gblup_prediction_all_6001_7000.rds")
+T18_1_gblup_prediction_all_7001_8000=readRDS(file="T18_1_gblup_prediction_all_7001_8000.rds")
+T18_1_gblup_prediction_all_8001_9000=readRDS(file="T18_1_gblup_prediction_all_8001_9000.rds")
+T18_1_gblup_prediction_all_9001_10000=readRDS(file="T18_1_gblup_prediction_all_9001_10000.rds")
+T18_1_gblup_prediction_all_10001_11000=readRDS(file="T18_1_gblup_prediction_all_10001_11000.rds")
+T18_1_gblup_prediction_all_11001_12419=readRDS(file="T18_1_gblup_prediction_all_11001_12419.rds")
+T18_1_gblup_prediction_all=c(T18_1_gblup_prediction_all_1_1000,T18_1_gblup_prediction_all_1001_2000,T18_1_gblup_prediction_all_2001_3000,T18_1_gblup_prediction_all_3001_4000,T18_1_gblup_prediction_all_4001_5000,T18_1_gblup_prediction_all_5001_6000,T18_1_gblup_prediction_all_6001_7000,T18_1_gblup_prediction_all_7001_8000,T18_1_gblup_prediction_all_8001_9000,T18_1_gblup_prediction_all_9001_10000,T18_1_gblup_prediction_all_10001_11000,T18_1_gblup_prediction_all_11001_12419)
+
+T18_1_gblup_variances_all_1_1000=readRDS(file="T18_1_gblup_variances_all_1_1000.rds")
+T18_1_gblup_variances_all_1001_2000=readRDS(file="T18_1_gblup_variances_all_1001_2000.rds")
+T18_1_gblup_variances_all_2001_3000=readRDS(file="T18_1_gblup_variances_all_2001_3000.rds")
+T18_1_gblup_variances_all_3001_4000=readRDS(file="T18_1_gblup_variances_all_3001_4000.rds")
+T18_1_gblup_variances_all_4001_5000=readRDS(file="T18_1_gblup_variances_all_4001_5000.rds")
+T18_1_gblup_variances_all_5001_6000=readRDS(file="T18_1_gblup_variances_all_5001_6000.rds")
+T18_1_gblup_variances_all_6001_7000=readRDS(file="T18_1_gblup_variances_all_6001_7000.rds")
+T18_1_gblup_variances_all_7001_8000=readRDS(file="T18_1_gblup_variances_all_7001_8000.rds")
+T18_1_gblup_variances_all_8001_9000=readRDS(file="T18_1_gblup_variances_all_8001_9000.rds")
+T18_1_gblup_variances_all_9001_10000=readRDS(file="T18_1_gblup_variances_all_9001_10000.rds")
+T18_1_gblup_variances_all_10001_11000=readRDS(file="T18_1_gblup_variances_all_10001_11000.rds")
+T18_1_gblup_variances_all_11001_12419=readRDS(file="T18_1_gblup_variances_all_11001_12419.rds")
+T18_1_gblup_variances_all=c(T18_1_gblup_variances_all_1_1000,T18_1_gblup_variances_all_1001_2000,T18_1_gblup_variances_all_2001_3000,T18_1_gblup_variances_all_3001_4000,T18_1_gblup_variances_all_4001_5000,T18_1_gblup_variances_all_5001_6000,T18_1_gblup_variances_all_6001_7000,T18_1_gblup_variances_all_7001_8000,T18_1_gblup_variances_all_8001_9000,T18_1_gblup_variances_all_9001_10000,T18_1_gblup_variances_all_10001_11000,T18_1_gblup_variances_all_11001_12419)
+
+saveRDS(T18_1_gblup_prediction_all,"T18_1_gblup_prediction_all.rds")
+saveRDS(T18_1_gblup_variances_all,"T18_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_1_gfblup_prediction_all_1_1000=readRDS(file="T18_1_gfblup_prediction_all_1_1000.rds")
+T18_1_gfblup_prediction_all_1001_2000=readRDS(file="T18_1_gfblup_prediction_all_1001_2000.rds")
+T18_1_gfblup_prediction_all_2001_3000=readRDS(file="T18_1_gfblup_prediction_all_2001_3000.rds")
+T18_1_gfblup_prediction_all_3001_4000=readRDS(file="T18_1_gfblup_prediction_all_3001_4000.rds")
+T18_1_gfblup_prediction_all_4001_5000=readRDS(file="T18_1_gfblup_prediction_all_4001_5000.rds")
+T18_1_gfblup_prediction_all_5001_6000=readRDS(file="T18_1_gfblup_prediction_all_5001_6000.rds")
+T18_1_gfblup_prediction_all_6001_7000=readRDS(file="T18_1_gfblup_prediction_all_6001_7000.rds")
+T18_1_gfblup_prediction_all_7001_8000=readRDS(file="T18_1_gfblup_prediction_all_7001_8000.rds")
+T18_1_gfblup_prediction_all_8001_9000=readRDS(file="T18_1_gfblup_prediction_all_8001_9000.rds")
+T18_1_gfblup_prediction_all_9001_10000=readRDS(file="T18_1_gfblup_prediction_all_9001_10000.rds")
+T18_1_gfblup_prediction_all_10001_11000=readRDS(file="T18_1_gfblup_prediction_all_10001_11000.rds")
+T18_1_gfblup_prediction_all_11001_12419=readRDS(file="T18_1_gfblup_prediction_all_11001_12419.rds")
+
+T18_1_gfblup_variances_all_1_1000=readRDS(file="T18_1_gfblup_variances_all_1_1000.rds")
+T18_1_gfblup_variances_all_1001_2000=readRDS(file="T18_1_gfblup_variances_all_1001_2000.rds")
+T18_1_gfblup_variances_all_2001_3000=readRDS(file="T18_1_gfblup_variances_all_2001_3000.rds")
+T18_1_gfblup_variances_all_3001_4000=readRDS(file="T18_1_gfblup_variances_all_3001_4000.rds")
+T18_1_gfblup_variances_all_4001_5000=readRDS(file="T18_1_gfblup_variances_all_4001_5000.rds")
+T18_1_gfblup_variances_all_5001_6000=readRDS(file="T18_1_gfblup_variances_all_5001_6000.rds")
+T18_1_gfblup_variances_all_6001_7000=readRDS(file="T18_1_gfblup_variances_all_6001_7000.rds")
+T18_1_gfblup_variances_all_7001_8000=readRDS(file="T18_1_gfblup_variances_all_7001_8000.rds")
+T18_1_gfblup_variances_all_8001_9000=readRDS(file="T18_1_gfblup_variances_all_8001_9000.rds")
+T18_1_gfblup_variances_all_9001_10000=readRDS(file="T18_1_gfblup_variances_all_9001_10000.rds")
+T18_1_gfblup_variances_all_10001_11000=readRDS(file="T18_1_gfblup_variances_all_10001_11000.rds")
+T18_1_gfblup_variances_all_11001_12419=readRDS(file="T18_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T18_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_1_gfblup_variances_all=rep(list(list()),cycles)
+T18_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_1_1000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_1001_2000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_2001_3000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_3001_4000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_4001_5000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_5001_6000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_6001_7000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_7001_8000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_8001_9000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_9001_10000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_10001_11000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_11001_12419[[r]])
+
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_1_1000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_1001_2000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_2001_3000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_3001_4000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_4001_5000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_5001_6000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_6001_7000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_7001_8000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_8001_9000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_9001_10000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_10001_11000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T18_1_gfblup_prediction_all,"T18_1_gfblup_prediction_all.rds")
+saveRDS(T18_1_gfblup_variances_all,"T18_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_2_gblup_prediction_all_1_1000=readRDS(file="T18_2_gblup_prediction_all_1_1000.rds")
+T18_2_gblup_prediction_all_1001_2000=readRDS(file="T18_2_gblup_prediction_all_1001_2000.rds")
+T18_2_gblup_prediction_all_2001_3000=readRDS(file="T18_2_gblup_prediction_all_2001_3000.rds")
+T18_2_gblup_prediction_all_3001_4000=readRDS(file="T18_2_gblup_prediction_all_3001_4000.rds")
+T18_2_gblup_prediction_all_4001_5000=readRDS(file="T18_2_gblup_prediction_all_4001_5000.rds")
+T18_2_gblup_prediction_all_5001_6000=readRDS(file="T18_2_gblup_prediction_all_5001_6000.rds")
+T18_2_gblup_prediction_all_6001_7000=readRDS(file="T18_2_gblup_prediction_all_6001_7000.rds")
+T18_2_gblup_prediction_all_7001_8000=readRDS(file="T18_2_gblup_prediction_all_7001_8000.rds")
+T18_2_gblup_prediction_all_8001_9000=readRDS(file="T18_2_gblup_prediction_all_8001_9000.rds")
+T18_2_gblup_prediction_all_9001_10000=readRDS(file="T18_2_gblup_prediction_all_9001_10000.rds")
+T18_2_gblup_prediction_all_10001_11000=readRDS(file="T18_2_gblup_prediction_all_10001_11000.rds")
+T18_2_gblup_prediction_all_11001_12419=readRDS(file="T18_2_gblup_prediction_all_11001_12419.rds")
+T18_2_gblup_prediction_all=c(T18_2_gblup_prediction_all_1_1000,T18_2_gblup_prediction_all_1001_2000,T18_2_gblup_prediction_all_2001_3000,T18_2_gblup_prediction_all_3001_4000,T18_2_gblup_prediction_all_4001_5000,T18_2_gblup_prediction_all_5001_6000,T18_2_gblup_prediction_all_6001_7000,T18_2_gblup_prediction_all_7001_8000,T18_2_gblup_prediction_all_8001_9000,T18_2_gblup_prediction_all_9001_10000,T18_2_gblup_prediction_all_10001_11000,T18_2_gblup_prediction_all_11001_12419)
+
+T18_2_gblup_variances_all_1_1000=readRDS(file="T18_2_gblup_variances_all_1_1000.rds")
+T18_2_gblup_variances_all_1001_2000=readRDS(file="T18_2_gblup_variances_all_1001_2000.rds")
+T18_2_gblup_variances_all_2001_3000=readRDS(file="T18_2_gblup_variances_all_2001_3000.rds")
+T18_2_gblup_variances_all_3001_4000=readRDS(file="T18_2_gblup_variances_all_3001_4000.rds")
+T18_2_gblup_variances_all_4001_5000=readRDS(file="T18_2_gblup_variances_all_4001_5000.rds")
+T18_2_gblup_variances_all_5001_6000=readRDS(file="T18_2_gblup_variances_all_5001_6000.rds")
+T18_2_gblup_variances_all_6001_7000=readRDS(file="T18_2_gblup_variances_all_6001_7000.rds")
+T18_2_gblup_variances_all_7001_8000=readRDS(file="T18_2_gblup_variances_all_7001_8000.rds")
+T18_2_gblup_variances_all_8001_9000=readRDS(file="T18_2_gblup_variances_all_8001_9000.rds")
+T18_2_gblup_variances_all_9001_10000=readRDS(file="T18_2_gblup_variances_all_9001_10000.rds")
+T18_2_gblup_variances_all_10001_11000=readRDS(file="T18_2_gblup_variances_all_10001_11000.rds")
+T18_2_gblup_variances_all_11001_12419=readRDS(file="T18_2_gblup_variances_all_11001_12419.rds")
+T18_2_gblup_variances_all=c(T18_2_gblup_variances_all_1_1000,T18_2_gblup_variances_all_1001_2000,T18_2_gblup_variances_all_2001_3000,T18_2_gblup_variances_all_3001_4000,T18_2_gblup_variances_all_4001_5000,T18_2_gblup_variances_all_5001_6000,T18_2_gblup_variances_all_6001_7000,T18_2_gblup_variances_all_7001_8000,T18_2_gblup_variances_all_8001_9000,T18_2_gblup_variances_all_9001_10000,T18_2_gblup_variances_all_10001_11000,T18_2_gblup_variances_all_11001_12419)
+
+saveRDS(T18_2_gblup_prediction_all,"T18_2_gblup_prediction_all.rds")
+saveRDS(T18_2_gblup_variances_all,"T18_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_2_gfblup_prediction_all_1_1000=readRDS(file="T18_2_gfblup_prediction_all_1_1000.rds")
+T18_2_gfblup_prediction_all_1001_2000=readRDS(file="T18_2_gfblup_prediction_all_1001_2000.rds")
+T18_2_gfblup_prediction_all_2001_3000=readRDS(file="T18_2_gfblup_prediction_all_2001_3000.rds")
+T18_2_gfblup_prediction_all_3001_4000=readRDS(file="T18_2_gfblup_prediction_all_3001_4000.rds")
+T18_2_gfblup_prediction_all_4001_5000=readRDS(file="T18_2_gfblup_prediction_all_4001_5000.rds")
+T18_2_gfblup_prediction_all_5001_6000=readRDS(file="T18_2_gfblup_prediction_all_5001_6000.rds")
+T18_2_gfblup_prediction_all_6001_7000=readRDS(file="T18_2_gfblup_prediction_all_6001_7000.rds")
+T18_2_gfblup_prediction_all_7001_8000=readRDS(file="T18_2_gfblup_prediction_all_7001_8000.rds")
+T18_2_gfblup_prediction_all_8001_9000=readRDS(file="T18_2_gfblup_prediction_all_8001_9000.rds")
+T18_2_gfblup_prediction_all_9001_10000=readRDS(file="T18_2_gfblup_prediction_all_9001_10000.rds")
+T18_2_gfblup_prediction_all_10001_11000=readRDS(file="T18_2_gfblup_prediction_all_10001_11000.rds")
+T18_2_gfblup_prediction_all_11001_12419=readRDS(file="T18_2_gfblup_prediction_all_11001_12419.rds")
+
+T18_2_gfblup_variances_all_1_1000=readRDS(file="T18_2_gfblup_variances_all_1_1000.rds")
+T18_2_gfblup_variances_all_1001_2000=readRDS(file="T18_2_gfblup_variances_all_1001_2000.rds")
+T18_2_gfblup_variances_all_2001_3000=readRDS(file="T18_2_gfblup_variances_all_2001_3000.rds")
+T18_2_gfblup_variances_all_3001_4000=readRDS(file="T18_2_gfblup_variances_all_3001_4000.rds")
+T18_2_gfblup_variances_all_4001_5000=readRDS(file="T18_2_gfblup_variances_all_4001_5000.rds")
+T18_2_gfblup_variances_all_5001_6000=readRDS(file="T18_2_gfblup_variances_all_5001_6000.rds")
+T18_2_gfblup_variances_all_6001_7000=readRDS(file="T18_2_gfblup_variances_all_6001_7000.rds")
+T18_2_gfblup_variances_all_7001_8000=readRDS(file="T18_2_gfblup_variances_all_7001_8000.rds")
+T18_2_gfblup_variances_all_8001_9000=readRDS(file="T18_2_gfblup_variances_all_8001_9000.rds")
+T18_2_gfblup_variances_all_9001_10000=readRDS(file="T18_2_gfblup_variances_all_9001_10000.rds")
+T18_2_gfblup_variances_all_10001_11000=readRDS(file="T18_2_gfblup_variances_all_10001_11000.rds")
+T18_2_gfblup_variances_all_11001_12419=readRDS(file="T18_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T18_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_2_gfblup_variances_all=rep(list(list()),cycles)
+T18_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_1_1000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_1001_2000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_2001_3000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_3001_4000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_4001_5000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_5001_6000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_6001_7000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_7001_8000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_8001_9000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_9001_10000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_10001_11000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_11001_12419[[r]])
+
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_1_1000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_1001_2000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_2001_3000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_3001_4000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_4001_5000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_5001_6000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_6001_7000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_7001_8000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_8001_9000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_9001_10000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_10001_11000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T18_2_gfblup_prediction_all,"T18_2_gfblup_prediction_all.rds")
+saveRDS(T18_2_gfblup_variances_all,"T18_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_3_gblup_prediction_all_1_1000=readRDS(file="T18_3_gblup_prediction_all_1_1000.rds")
+T18_3_gblup_prediction_all_1001_2000=readRDS(file="T18_3_gblup_prediction_all_1001_2000.rds")
+T18_3_gblup_prediction_all_2001_3000=readRDS(file="T18_3_gblup_prediction_all_2001_3000.rds")
+T18_3_gblup_prediction_all_3001_4000=readRDS(file="T18_3_gblup_prediction_all_3001_4000.rds")
+T18_3_gblup_prediction_all_4001_5000=readRDS(file="T18_3_gblup_prediction_all_4001_5000.rds")
+T18_3_gblup_prediction_all_5001_6000=readRDS(file="T18_3_gblup_prediction_all_5001_6000.rds")
+T18_3_gblup_prediction_all_6001_7000=readRDS(file="T18_3_gblup_prediction_all_6001_7000.rds")
+T18_3_gblup_prediction_all_7001_8000=readRDS(file="T18_3_gblup_prediction_all_7001_8000.rds")
+T18_3_gblup_prediction_all_8001_9000=readRDS(file="T18_3_gblup_prediction_all_8001_9000.rds")
+T18_3_gblup_prediction_all_9001_10000=readRDS(file="T18_3_gblup_prediction_all_9001_10000.rds")
+T18_3_gblup_prediction_all_10001_11000=readRDS(file="T18_3_gblup_prediction_all_10001_11000.rds")
+T18_3_gblup_prediction_all_11001_12419=readRDS(file="T18_3_gblup_prediction_all_11001_12419.rds")
+T18_3_gblup_prediction_all=c(T18_3_gblup_prediction_all_1_1000,T18_3_gblup_prediction_all_1001_2000,T18_3_gblup_prediction_all_2001_3000,T18_3_gblup_prediction_all_3001_4000,T18_3_gblup_prediction_all_4001_5000,T18_3_gblup_prediction_all_5001_6000,T18_3_gblup_prediction_all_6001_7000,T18_3_gblup_prediction_all_7001_8000,T18_3_gblup_prediction_all_8001_9000,T18_3_gblup_prediction_all_9001_10000,T18_3_gblup_prediction_all_10001_11000,T18_3_gblup_prediction_all_11001_12419)
+
+T18_3_gblup_variances_all_1_1000=readRDS(file="T18_3_gblup_variances_all_1_1000.rds")
+T18_3_gblup_variances_all_1001_2000=readRDS(file="T18_3_gblup_variances_all_1001_2000.rds")
+T18_3_gblup_variances_all_2001_3000=readRDS(file="T18_3_gblup_variances_all_2001_3000.rds")
+T18_3_gblup_variances_all_3001_4000=readRDS(file="T18_3_gblup_variances_all_3001_4000.rds")
+T18_3_gblup_variances_all_4001_5000=readRDS(file="T18_3_gblup_variances_all_4001_5000.rds")
+T18_3_gblup_variances_all_5001_6000=readRDS(file="T18_3_gblup_variances_all_5001_6000.rds")
+T18_3_gblup_variances_all_6001_7000=readRDS(file="T18_3_gblup_variances_all_6001_7000.rds")
+T18_3_gblup_variances_all_7001_8000=readRDS(file="T18_3_gblup_variances_all_7001_8000.rds")
+T18_3_gblup_variances_all_8001_9000=readRDS(file="T18_3_gblup_variances_all_8001_9000.rds")
+T18_3_gblup_variances_all_9001_10000=readRDS(file="T18_3_gblup_variances_all_9001_10000.rds")
+T18_3_gblup_variances_all_10001_11000=readRDS(file="T18_3_gblup_variances_all_10001_11000.rds")
+T18_3_gblup_variances_all_11001_12419=readRDS(file="T18_3_gblup_variances_all_11001_12419.rds")
+T18_3_gblup_variances_all=c(T18_3_gblup_variances_all_1_1000,T18_3_gblup_variances_all_1001_2000,T18_3_gblup_variances_all_2001_3000,T18_3_gblup_variances_all_3001_4000,T18_3_gblup_variances_all_4001_5000,T18_3_gblup_variances_all_5001_6000,T18_3_gblup_variances_all_6001_7000,T18_3_gblup_variances_all_7001_8000,T18_3_gblup_variances_all_8001_9000,T18_3_gblup_variances_all_9001_10000,T18_3_gblup_variances_all_10001_11000,T18_3_gblup_variances_all_11001_12419)
+
+saveRDS(T18_3_gblup_prediction_all,"T18_3_gblup_prediction_all.rds")
+saveRDS(T18_3_gblup_variances_all,"T18_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_3_gfblup_prediction_all_1_1000=readRDS(file="T18_3_gfblup_prediction_all_1_1000.rds")
+T18_3_gfblup_prediction_all_1001_2000=readRDS(file="T18_3_gfblup_prediction_all_1001_2000.rds")
+T18_3_gfblup_prediction_all_2001_3000=readRDS(file="T18_3_gfblup_prediction_all_2001_3000.rds")
+T18_3_gfblup_prediction_all_3001_4000=readRDS(file="T18_3_gfblup_prediction_all_3001_4000.rds")
+T18_3_gfblup_prediction_all_4001_5000=readRDS(file="T18_3_gfblup_prediction_all_4001_5000.rds")
+T18_3_gfblup_prediction_all_5001_6000=readRDS(file="T18_3_gfblup_prediction_all_5001_6000.rds")
+T18_3_gfblup_prediction_all_6001_7000=readRDS(file="T18_3_gfblup_prediction_all_6001_7000.rds")
+T18_3_gfblup_prediction_all_7001_8000=readRDS(file="T18_3_gfblup_prediction_all_7001_8000.rds")
+T18_3_gfblup_prediction_all_8001_9000=readRDS(file="T18_3_gfblup_prediction_all_8001_9000.rds")
+T18_3_gfblup_prediction_all_9001_10000=readRDS(file="T18_3_gfblup_prediction_all_9001_10000.rds")
+T18_3_gfblup_prediction_all_10001_11000=readRDS(file="T18_3_gfblup_prediction_all_10001_11000.rds")
+T18_3_gfblup_prediction_all_11001_12419=readRDS(file="T18_3_gfblup_prediction_all_11001_12419.rds")
+
+T18_3_gfblup_variances_all_1_1000=readRDS(file="T18_3_gfblup_variances_all_1_1000.rds")
+T18_3_gfblup_variances_all_1001_2000=readRDS(file="T18_3_gfblup_variances_all_1001_2000.rds")
+T18_3_gfblup_variances_all_2001_3000=readRDS(file="T18_3_gfblup_variances_all_2001_3000.rds")
+T18_3_gfblup_variances_all_3001_4000=readRDS(file="T18_3_gfblup_variances_all_3001_4000.rds")
+T18_3_gfblup_variances_all_4001_5000=readRDS(file="T18_3_gfblup_variances_all_4001_5000.rds")
+T18_3_gfblup_variances_all_5001_6000=readRDS(file="T18_3_gfblup_variances_all_5001_6000.rds")
+T18_3_gfblup_variances_all_6001_7000=readRDS(file="T18_3_gfblup_variances_all_6001_7000.rds")
+T18_3_gfblup_variances_all_7001_8000=readRDS(file="T18_3_gfblup_variances_all_7001_8000.rds")
+T18_3_gfblup_variances_all_8001_9000=readRDS(file="T18_3_gfblup_variances_all_8001_9000.rds")
+T18_3_gfblup_variances_all_9001_10000=readRDS(file="T18_3_gfblup_variances_all_9001_10000.rds")
+T18_3_gfblup_variances_all_10001_11000=readRDS(file="T18_3_gfblup_variances_all_10001_11000.rds")
+T18_3_gfblup_variances_all_11001_12419=readRDS(file="T18_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T18_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_3_gfblup_variances_all=rep(list(list()),cycles)
+T18_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_1_1000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_1001_2000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_2001_3000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_3001_4000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_4001_5000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_5001_6000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_6001_7000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_7001_8000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_8001_9000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_9001_10000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_10001_11000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_11001_12419[[r]])
+
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_1_1000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_1001_2000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_2001_3000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_3001_4000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_4001_5000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_5001_6000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_6001_7000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_7001_8000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_8001_9000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_9001_10000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_10001_11000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T18_3_gfblup_prediction_all,"T18_3_gfblup_prediction_all.rds")
+saveRDS(T18_3_gfblup_variances_all,"T18_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_4_gblup_prediction_all_1_1000=readRDS(file="T18_4_gblup_prediction_all_1_1000.rds")
+T18_4_gblup_prediction_all_1001_2000=readRDS(file="T18_4_gblup_prediction_all_1001_2000.rds")
+T18_4_gblup_prediction_all_2001_3000=readRDS(file="T18_4_gblup_prediction_all_2001_3000.rds")
+T18_4_gblup_prediction_all_3001_4000=readRDS(file="T18_4_gblup_prediction_all_3001_4000.rds")
+T18_4_gblup_prediction_all_4001_5000=readRDS(file="T18_4_gblup_prediction_all_4001_5000.rds")
+T18_4_gblup_prediction_all_5001_6000=readRDS(file="T18_4_gblup_prediction_all_5001_6000.rds")
+T18_4_gblup_prediction_all_6001_7000=readRDS(file="T18_4_gblup_prediction_all_6001_7000.rds")
+T18_4_gblup_prediction_all_7001_8000=readRDS(file="T18_4_gblup_prediction_all_7001_8000.rds")
+T18_4_gblup_prediction_all_8001_9000=readRDS(file="T18_4_gblup_prediction_all_8001_9000.rds")
+T18_4_gblup_prediction_all_9001_10000=readRDS(file="T18_4_gblup_prediction_all_9001_10000.rds")
+T18_4_gblup_prediction_all_10001_11000=readRDS(file="T18_4_gblup_prediction_all_10001_11000.rds")
+T18_4_gblup_prediction_all_11001_12419=readRDS(file="T18_4_gblup_prediction_all_11001_12419.rds")
+T18_4_gblup_prediction_all=c(T18_4_gblup_prediction_all_1_1000,T18_4_gblup_prediction_all_1001_2000,T18_4_gblup_prediction_all_2001_3000,T18_4_gblup_prediction_all_3001_4000,T18_4_gblup_prediction_all_4001_5000,T18_4_gblup_prediction_all_5001_6000,T18_4_gblup_prediction_all_6001_7000,T18_4_gblup_prediction_all_7001_8000,T18_4_gblup_prediction_all_8001_9000,T18_4_gblup_prediction_all_9001_10000,T18_4_gblup_prediction_all_10001_11000,T18_4_gblup_prediction_all_11001_12419)
+
+T18_4_gblup_variances_all_1_1000=readRDS(file="T18_4_gblup_variances_all_1_1000.rds")
+T18_4_gblup_variances_all_1001_2000=readRDS(file="T18_4_gblup_variances_all_1001_2000.rds")
+T18_4_gblup_variances_all_2001_3000=readRDS(file="T18_4_gblup_variances_all_2001_3000.rds")
+T18_4_gblup_variances_all_3001_4000=readRDS(file="T18_4_gblup_variances_all_3001_4000.rds")
+T18_4_gblup_variances_all_4001_5000=readRDS(file="T18_4_gblup_variances_all_4001_5000.rds")
+T18_4_gblup_variances_all_5001_6000=readRDS(file="T18_4_gblup_variances_all_5001_6000.rds")
+T18_4_gblup_variances_all_6001_7000=readRDS(file="T18_4_gblup_variances_all_6001_7000.rds")
+T18_4_gblup_variances_all_7001_8000=readRDS(file="T18_4_gblup_variances_all_7001_8000.rds")
+T18_4_gblup_variances_all_8001_9000=readRDS(file="T18_4_gblup_variances_all_8001_9000.rds")
+T18_4_gblup_variances_all_9001_10000=readRDS(file="T18_4_gblup_variances_all_9001_10000.rds")
+T18_4_gblup_variances_all_10001_11000=readRDS(file="T18_4_gblup_variances_all_10001_11000.rds")
+T18_4_gblup_variances_all_11001_12419=readRDS(file="T18_4_gblup_variances_all_11001_12419.rds")
+T18_4_gblup_variances_all=c(T18_4_gblup_variances_all_1_1000,T18_4_gblup_variances_all_1001_2000,T18_4_gblup_variances_all_2001_3000,T18_4_gblup_variances_all_3001_4000,T18_4_gblup_variances_all_4001_5000,T18_4_gblup_variances_all_5001_6000,T18_4_gblup_variances_all_6001_7000,T18_4_gblup_variances_all_7001_8000,T18_4_gblup_variances_all_8001_9000,T18_4_gblup_variances_all_9001_10000,T18_4_gblup_variances_all_10001_11000,T18_4_gblup_variances_all_11001_12419)
+
+saveRDS(T18_4_gblup_prediction_all,"T18_4_gblup_prediction_all.rds")
+saveRDS(T18_4_gblup_variances_all,"T18_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_4_gfblup_prediction_all_1_1000=readRDS(file="T18_4_gfblup_prediction_all_1_1000.rds")
+T18_4_gfblup_prediction_all_1001_2000=readRDS(file="T18_4_gfblup_prediction_all_1001_2000.rds")
+T18_4_gfblup_prediction_all_2001_3000=readRDS(file="T18_4_gfblup_prediction_all_2001_3000.rds")
+T18_4_gfblup_prediction_all_3001_4000=readRDS(file="T18_4_gfblup_prediction_all_3001_4000.rds")
+T18_4_gfblup_prediction_all_4001_5000=readRDS(file="T18_4_gfblup_prediction_all_4001_5000.rds")
+T18_4_gfblup_prediction_all_5001_6000=readRDS(file="T18_4_gfblup_prediction_all_5001_6000.rds")
+T18_4_gfblup_prediction_all_6001_7000=readRDS(file="T18_4_gfblup_prediction_all_6001_7000.rds")
+T18_4_gfblup_prediction_all_7001_8000=readRDS(file="T18_4_gfblup_prediction_all_7001_8000.rds")
+T18_4_gfblup_prediction_all_8001_9000=readRDS(file="T18_4_gfblup_prediction_all_8001_9000.rds")
+T18_4_gfblup_prediction_all_9001_10000=readRDS(file="T18_4_gfblup_prediction_all_9001_10000.rds")
+T18_4_gfblup_prediction_all_10001_11000=readRDS(file="T18_4_gfblup_prediction_all_10001_11000.rds")
+T18_4_gfblup_prediction_all_11001_12419=readRDS(file="T18_4_gfblup_prediction_all_11001_12419.rds")
+
+T18_4_gfblup_variances_all_1_1000=readRDS(file="T18_4_gfblup_variances_all_1_1000.rds")
+T18_4_gfblup_variances_all_1001_2000=readRDS(file="T18_4_gfblup_variances_all_1001_2000.rds")
+T18_4_gfblup_variances_all_2001_3000=readRDS(file="T18_4_gfblup_variances_all_2001_3000.rds")
+T18_4_gfblup_variances_all_3001_4000=readRDS(file="T18_4_gfblup_variances_all_3001_4000.rds")
+T18_4_gfblup_variances_all_4001_5000=readRDS(file="T18_4_gfblup_variances_all_4001_5000.rds")
+T18_4_gfblup_variances_all_5001_6000=readRDS(file="T18_4_gfblup_variances_all_5001_6000.rds")
+T18_4_gfblup_variances_all_6001_7000=readRDS(file="T18_4_gfblup_variances_all_6001_7000.rds")
+T18_4_gfblup_variances_all_7001_8000=readRDS(file="T18_4_gfblup_variances_all_7001_8000.rds")
+T18_4_gfblup_variances_all_8001_9000=readRDS(file="T18_4_gfblup_variances_all_8001_9000.rds")
+T18_4_gfblup_variances_all_9001_10000=readRDS(file="T18_4_gfblup_variances_all_9001_10000.rds")
+T18_4_gfblup_variances_all_10001_11000=readRDS(file="T18_4_gfblup_variances_all_10001_11000.rds")
+T18_4_gfblup_variances_all_11001_12419=readRDS(file="T18_4_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T18_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_4_gfblup_variances_all=rep(list(list()),cycles)
+T18_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_1_1000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_1001_2000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_2001_3000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_3001_4000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_4001_5000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_5001_6000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_6001_7000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_7001_8000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_8001_9000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_9001_10000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_10001_11000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_11001_12419[[r]])
+
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_1_1000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_1001_2000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_2001_3000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_3001_4000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_4001_5000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_5001_6000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_6001_7000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_7001_8000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_8001_9000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_9001_10000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_10001_11000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T18_4_gfblup_prediction_all,"T18_4_gfblup_prediction_all.rds")
+saveRDS(T18_4_gfblup_variances_all,"T18_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_5_gblup_prediction_all_1_1000=readRDS(file="T18_5_gblup_prediction_all_1_1000.rds")
+T18_5_gblup_prediction_all_1001_2000=readRDS(file="T18_5_gblup_prediction_all_1001_2000.rds")
+T18_5_gblup_prediction_all_2001_3000=readRDS(file="T18_5_gblup_prediction_all_2001_3000.rds")
+T18_5_gblup_prediction_all_3001_4000=readRDS(file="T18_5_gblup_prediction_all_3001_4000.rds")
+T18_5_gblup_prediction_all_4001_5000=readRDS(file="T18_5_gblup_prediction_all_4001_5000.rds")
+T18_5_gblup_prediction_all_5001_6000=readRDS(file="T18_5_gblup_prediction_all_5001_6000.rds")
+T18_5_gblup_prediction_all_6001_7000=readRDS(file="T18_5_gblup_prediction_all_6001_7000.rds")
+T18_5_gblup_prediction_all_7001_8000=readRDS(file="T18_5_gblup_prediction_all_7001_8000.rds")
+T18_5_gblup_prediction_all_8001_9000=readRDS(file="T18_5_gblup_prediction_all_8001_9000.rds")
+T18_5_gblup_prediction_all_9001_10000=readRDS(file="T18_5_gblup_prediction_all_9001_10000.rds")
+T18_5_gblup_prediction_all_10001_11000=readRDS(file="T18_5_gblup_prediction_all_10001_11000.rds")
+T18_5_gblup_prediction_all_11001_12419=readRDS(file="T18_5_gblup_prediction_all_11001_12419.rds")
+T18_5_gblup_prediction_all=c(T18_5_gblup_prediction_all_1_1000,T18_5_gblup_prediction_all_1001_2000,T18_5_gblup_prediction_all_2001_3000,T18_5_gblup_prediction_all_3001_4000,T18_5_gblup_prediction_all_4001_5000,T18_5_gblup_prediction_all_5001_6000,T18_5_gblup_prediction_all_6001_7000,T18_5_gblup_prediction_all_7001_8000,T18_5_gblup_prediction_all_8001_9000,T18_5_gblup_prediction_all_9001_10000,T18_5_gblup_prediction_all_10001_11000,T18_5_gblup_prediction_all_11001_12419)
+
+T18_5_gblup_variances_all_1_1000=readRDS(file="T18_5_gblup_variances_all_1_1000.rds")
+T18_5_gblup_variances_all_1001_2000=readRDS(file="T18_5_gblup_variances_all_1001_2000.rds")
+T18_5_gblup_variances_all_2001_3000=readRDS(file="T18_5_gblup_variances_all_2001_3000.rds")
+T18_5_gblup_variances_all_3001_4000=readRDS(file="T18_5_gblup_variances_all_3001_4000.rds")
+T18_5_gblup_variances_all_4001_5000=readRDS(file="T18_5_gblup_variances_all_4001_5000.rds")
+T18_5_gblup_variances_all_5001_6000=readRDS(file="T18_5_gblup_variances_all_5001_6000.rds")
+T18_5_gblup_variances_all_6001_7000=readRDS(file="T18_5_gblup_variances_all_6001_7000.rds")
+T18_5_gblup_variances_all_7001_8000=readRDS(file="T18_5_gblup_variances_all_7001_8000.rds")
+T18_5_gblup_variances_all_8001_9000=readRDS(file="T18_5_gblup_variances_all_8001_9000.rds")
+T18_5_gblup_variances_all_9001_10000=readRDS(file="T18_5_gblup_variances_all_9001_10000.rds")
+T18_5_gblup_variances_all_10001_11000=readRDS(file="T18_5_gblup_variances_all_10001_11000.rds")
+T18_5_gblup_variances_all_11001_12419=readRDS(file="T18_5_gblup_variances_all_11001_12419.rds")
+T18_5_gblup_variances_all=c(T18_5_gblup_variances_all_1_1000,T18_5_gblup_variances_all_1001_2000,T18_5_gblup_variances_all_2001_3000,T18_5_gblup_variances_all_3001_4000,T18_5_gblup_variances_all_4001_5000,T18_5_gblup_variances_all_5001_6000,T18_5_gblup_variances_all_6001_7000,T18_5_gblup_variances_all_7001_8000,T18_5_gblup_variances_all_8001_9000,T18_5_gblup_variances_all_9001_10000,T18_5_gblup_variances_all_10001_11000,T18_5_gblup_variances_all_11001_12419)
+
+saveRDS(T18_5_gblup_prediction_all,"T18_5_gblup_prediction_all.rds")
+saveRDS(T18_5_gblup_variances_all,"T18_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_5_gfblup_prediction_all_1_1000=readRDS(file="T18_5_gfblup_prediction_all_1_1000.rds")
+T18_5_gfblup_prediction_all_1001_2000=readRDS(file="T18_5_gfblup_prediction_all_1001_2000.rds")
+T18_5_gfblup_prediction_all_2001_3000=readRDS(file="T18_5_gfblup_prediction_all_2001_3000.rds")
+T18_5_gfblup_prediction_all_3001_4000=readRDS(file="T18_5_gfblup_prediction_all_3001_4000.rds")
+T18_5_gfblup_prediction_all_4001_5000=readRDS(file="T18_5_gfblup_prediction_all_4001_5000.rds")
+T18_5_gfblup_prediction_all_5001_6000=readRDS(file="T18_5_gfblup_prediction_all_5001_6000.rds")
+T18_5_gfblup_prediction_all_6001_7000=readRDS(file="T18_5_gfblup_prediction_all_6001_7000.rds")
+T18_5_gfblup_prediction_all_7001_8000=readRDS(file="T18_5_gfblup_prediction_all_7001_8000.rds")
+T18_5_gfblup_prediction_all_8001_9000=readRDS(file="T18_5_gfblup_prediction_all_8001_9000.rds")
+T18_5_gfblup_prediction_all_9001_10000=readRDS(file="T18_5_gfblup_prediction_all_9001_10000.rds")
+T18_5_gfblup_prediction_all_10001_11000=readRDS(file="T18_5_gfblup_prediction_all_10001_11000.rds")
+T18_5_gfblup_prediction_all_11001_12419=readRDS(file="T18_5_gfblup_prediction_all_11001_12419.rds")
+
+T18_5_gfblup_variances_all_1_1000=readRDS(file="T18_5_gfblup_variances_all_1_1000.rds")
+T18_5_gfblup_variances_all_1001_2000=readRDS(file="T18_5_gfblup_variances_all_1001_2000.rds")
+T18_5_gfblup_variances_all_2001_3000=readRDS(file="T18_5_gfblup_variances_all_2001_3000.rds")
+T18_5_gfblup_variances_all_3001_4000=readRDS(file="T18_5_gfblup_variances_all_3001_4000.rds")
+T18_5_gfblup_variances_all_4001_5000=readRDS(file="T18_5_gfblup_variances_all_4001_5000.rds")
+T18_5_gfblup_variances_all_5001_6000=readRDS(file="T18_5_gfblup_variances_all_5001_6000.rds")
+T18_5_gfblup_variances_all_6001_7000=readRDS(file="T18_5_gfblup_variances_all_6001_7000.rds")
+T18_5_gfblup_variances_all_7001_8000=readRDS(file="T18_5_gfblup_variances_all_7001_8000.rds")
+T18_5_gfblup_variances_all_8001_9000=readRDS(file="T18_5_gfblup_variances_all_8001_9000.rds")
+T18_5_gfblup_variances_all_9001_10000=readRDS(file="T18_5_gfblup_variances_all_9001_10000.rds")
+T18_5_gfblup_variances_all_10001_11000=readRDS(file="T18_5_gfblup_variances_all_10001_11000.rds")
+T18_5_gfblup_variances_all_11001_12419=readRDS(file="T18_5_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T18_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_5_gfblup_variances_all=rep(list(list()),cycles)
+T18_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_1_1000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_1001_2000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_2001_3000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_3001_4000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_4001_5000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_5001_6000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_6001_7000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_7001_8000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_8001_9000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_9001_10000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_10001_11000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_11001_12419[[r]])
+
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_1_1000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_1001_2000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_2001_3000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_3001_4000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_4001_5000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_5001_6000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_6001_7000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_7001_8000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_8001_9000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_9001_10000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_10001_11000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T18_5_gfblup_prediction_all,"T18_5_gfblup_prediction_all.rds")
+saveRDS(T18_5_gfblup_variances_all,"T18_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_6_gblup_prediction_all_1_1000=readRDS(file="T18_6_gblup_prediction_all_1_1000.rds")
+T18_6_gblup_prediction_all_1001_2000=readRDS(file="T18_6_gblup_prediction_all_1001_2000.rds")
+T18_6_gblup_prediction_all_2001_3000=readRDS(file="T18_6_gblup_prediction_all_2001_3000.rds")
+T18_6_gblup_prediction_all_3001_4000=readRDS(file="T18_6_gblup_prediction_all_3001_4000.rds")
+T18_6_gblup_prediction_all_4001_5000=readRDS(file="T18_6_gblup_prediction_all_4001_5000.rds")
+T18_6_gblup_prediction_all_5001_6000=readRDS(file="T18_6_gblup_prediction_all_5001_6000.rds")
+T18_6_gblup_prediction_all_6001_7000=readRDS(file="T18_6_gblup_prediction_all_6001_7000.rds")
+T18_6_gblup_prediction_all_7001_8000=readRDS(file="T18_6_gblup_prediction_all_7001_8000.rds")
+T18_6_gblup_prediction_all_8001_9000=readRDS(file="T18_6_gblup_prediction_all_8001_9000.rds")
+T18_6_gblup_prediction_all_9001_10000=readRDS(file="T18_6_gblup_prediction_all_9001_10000.rds")
+T18_6_gblup_prediction_all_10001_11000=readRDS(file="T18_6_gblup_prediction_all_10001_11000.rds")
+T18_6_gblup_prediction_all_11001_12419=readRDS(file="T18_6_gblup_prediction_all_11001_12419.rds")
+T18_6_gblup_prediction_all=c(T18_6_gblup_prediction_all_1_1000,T18_6_gblup_prediction_all_1001_2000,T18_6_gblup_prediction_all_2001_3000,T18_6_gblup_prediction_all_3001_4000,T18_6_gblup_prediction_all_4001_5000,T18_6_gblup_prediction_all_5001_6000,T18_6_gblup_prediction_all_6001_7000,T18_6_gblup_prediction_all_7001_8000,T18_6_gblup_prediction_all_8001_9000,T18_6_gblup_prediction_all_9001_10000,T18_6_gblup_prediction_all_10001_11000,T18_6_gblup_prediction_all_11001_12419)
+
+T18_6_gblup_variances_all_1_1000=readRDS(file="T18_6_gblup_variances_all_1_1000.rds")
+T18_6_gblup_variances_all_1001_2000=readRDS(file="T18_6_gblup_variances_all_1001_2000.rds")
+T18_6_gblup_variances_all_2001_3000=readRDS(file="T18_6_gblup_variances_all_2001_3000.rds")
+T18_6_gblup_variances_all_3001_4000=readRDS(file="T18_6_gblup_variances_all_3001_4000.rds")
+T18_6_gblup_variances_all_4001_5000=readRDS(file="T18_6_gblup_variances_all_4001_5000.rds")
+T18_6_gblup_variances_all_5001_6000=readRDS(file="T18_6_gblup_variances_all_5001_6000.rds")
+T18_6_gblup_variances_all_6001_7000=readRDS(file="T18_6_gblup_variances_all_6001_7000.rds")
+T18_6_gblup_variances_all_7001_8000=readRDS(file="T18_6_gblup_variances_all_7001_8000.rds")
+T18_6_gblup_variances_all_8001_9000=readRDS(file="T18_6_gblup_variances_all_8001_9000.rds")
+T18_6_gblup_variances_all_9001_10000=readRDS(file="T18_6_gblup_variances_all_9001_10000.rds")
+T18_6_gblup_variances_all_10001_11000=readRDS(file="T18_6_gblup_variances_all_10001_11000.rds")
+T18_6_gblup_variances_all_11001_12419=readRDS(file="T18_6_gblup_variances_all_11001_12419.rds")
+T18_6_gblup_variances_all=c(T18_6_gblup_variances_all_1_1000,T18_6_gblup_variances_all_1001_2000,T18_6_gblup_variances_all_2001_3000,T18_6_gblup_variances_all_3001_4000,T18_6_gblup_variances_all_4001_5000,T18_6_gblup_variances_all_5001_6000,T18_6_gblup_variances_all_6001_7000,T18_6_gblup_variances_all_7001_8000,T18_6_gblup_variances_all_8001_9000,T18_6_gblup_variances_all_9001_10000,T18_6_gblup_variances_all_10001_11000,T18_6_gblup_variances_all_11001_12419)
+
+saveRDS(T18_6_gblup_prediction_all,"T18_6_gblup_prediction_all.rds")
+saveRDS(T18_6_gblup_variances_all,"T18_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_6_gfblup_prediction_all_1_1000=readRDS(file="T18_6_gfblup_prediction_all_1_1000.rds")
+T18_6_gfblup_prediction_all_1001_2000=readRDS(file="T18_6_gfblup_prediction_all_1001_2000.rds")
+T18_6_gfblup_prediction_all_2001_3000=readRDS(file="T18_6_gfblup_prediction_all_2001_3000.rds")
+T18_6_gfblup_prediction_all_3001_4000=readRDS(file="T18_6_gfblup_prediction_all_3001_4000.rds")
+T18_6_gfblup_prediction_all_4001_5000=readRDS(file="T18_6_gfblup_prediction_all_4001_5000.rds")
+T18_6_gfblup_prediction_all_5001_6000=readRDS(file="T18_6_gfblup_prediction_all_5001_6000.rds")
+T18_6_gfblup_prediction_all_6001_7000=readRDS(file="T18_6_gfblup_prediction_all_6001_7000.rds")
+T18_6_gfblup_prediction_all_7001_8000=readRDS(file="T18_6_gfblup_prediction_all_7001_8000.rds")
+T18_6_gfblup_prediction_all_8001_9000=readRDS(file="T18_6_gfblup_prediction_all_8001_9000.rds")
+T18_6_gfblup_prediction_all_9001_10000=readRDS(file="T18_6_gfblup_prediction_all_9001_10000.rds")
+T18_6_gfblup_prediction_all_10001_11000=readRDS(file="T18_6_gfblup_prediction_all_10001_11000.rds")
+T18_6_gfblup_prediction_all_11001_12419=readRDS(file="T18_6_gfblup_prediction_all_11001_12419.rds")
+
+T18_6_gfblup_variances_all_1_1000=readRDS(file="T18_6_gfblup_variances_all_1_1000.rds")
+T18_6_gfblup_variances_all_1001_2000=readRDS(file="T18_6_gfblup_variances_all_1001_2000.rds")
+T18_6_gfblup_variances_all_2001_3000=readRDS(file="T18_6_gfblup_variances_all_2001_3000.rds")
+T18_6_gfblup_variances_all_3001_4000=readRDS(file="T18_6_gfblup_variances_all_3001_4000.rds")
+T18_6_gfblup_variances_all_4001_5000=readRDS(file="T18_6_gfblup_variances_all_4001_5000.rds")
+T18_6_gfblup_variances_all_5001_6000=readRDS(file="T18_6_gfblup_variances_all_5001_6000.rds")
+T18_6_gfblup_variances_all_6001_7000=readRDS(file="T18_6_gfblup_variances_all_6001_7000.rds")
+T18_6_gfblup_variances_all_7001_8000=readRDS(file="T18_6_gfblup_variances_all_7001_8000.rds")
+T18_6_gfblup_variances_all_8001_9000=readRDS(file="T18_6_gfblup_variances_all_8001_9000.rds")
+T18_6_gfblup_variances_all_9001_10000=readRDS(file="T18_6_gfblup_variances_all_9001_10000.rds")
+T18_6_gfblup_variances_all_10001_11000=readRDS(file="T18_6_gfblup_variances_all_10001_11000.rds")
+T18_6_gfblup_variances_all_11001_12419=readRDS(file="T18_6_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T18_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_6_gfblup_variances_all=rep(list(list()),cycles)
+T18_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_1_1000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_1001_2000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_2001_3000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_3001_4000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_4001_5000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_5001_6000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_6001_7000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_7001_8000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_8001_9000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_9001_10000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_10001_11000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_11001_12419[[r]])
+
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_1_1000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_1001_2000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_2001_3000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_3001_4000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_4001_5000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_5001_6000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_6001_7000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_7001_8000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_8001_9000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_9001_10000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_10001_11000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T18_6_gfblup_prediction_all,"T18_6_gfblup_prediction_all.rds")
+saveRDS(T18_6_gfblup_variances_all,"T18_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_7_gblup_prediction_all_1_1000=readRDS(file="T18_7_gblup_prediction_all_1_1000.rds")
+T18_7_gblup_prediction_all_1001_2000=readRDS(file="T18_7_gblup_prediction_all_1001_2000.rds")
+T18_7_gblup_prediction_all_2001_3000=readRDS(file="T18_7_gblup_prediction_all_2001_3000.rds")
+T18_7_gblup_prediction_all_3001_4000=readRDS(file="T18_7_gblup_prediction_all_3001_4000.rds")
+T18_7_gblup_prediction_all_4001_5000=readRDS(file="T18_7_gblup_prediction_all_4001_5000.rds")
+T18_7_gblup_prediction_all_5001_6000=readRDS(file="T18_7_gblup_prediction_all_5001_6000.rds")
+T18_7_gblup_prediction_all_6001_7000=readRDS(file="T18_7_gblup_prediction_all_6001_7000.rds")
+T18_7_gblup_prediction_all_7001_8000=readRDS(file="T18_7_gblup_prediction_all_7001_8000.rds")
+T18_7_gblup_prediction_all_8001_9000=readRDS(file="T18_7_gblup_prediction_all_8001_9000.rds")
+T18_7_gblup_prediction_all_9001_10000=readRDS(file="T18_7_gblup_prediction_all_9001_10000.rds")
+T18_7_gblup_prediction_all_10001_11000=readRDS(file="T18_7_gblup_prediction_all_10001_11000.rds")
+T18_7_gblup_prediction_all_11001_12419=readRDS(file="T18_7_gblup_prediction_all_11001_12419.rds")
+T18_7_gblup_prediction_all=c(T18_7_gblup_prediction_all_1_1000,T18_7_gblup_prediction_all_1001_2000,T18_7_gblup_prediction_all_2001_3000,T18_7_gblup_prediction_all_3001_4000,T18_7_gblup_prediction_all_4001_5000,T18_7_gblup_prediction_all_5001_6000,T18_7_gblup_prediction_all_6001_7000,T18_7_gblup_prediction_all_7001_8000,T18_7_gblup_prediction_all_8001_9000,T18_7_gblup_prediction_all_9001_10000,T18_7_gblup_prediction_all_10001_11000,T18_7_gblup_prediction_all_11001_12419)
+
+T18_7_gblup_variances_all_1_1000=readRDS(file="T18_7_gblup_variances_all_1_1000.rds")
+T18_7_gblup_variances_all_1001_2000=readRDS(file="T18_7_gblup_variances_all_1001_2000.rds")
+T18_7_gblup_variances_all_2001_3000=readRDS(file="T18_7_gblup_variances_all_2001_3000.rds")
+T18_7_gblup_variances_all_3001_4000=readRDS(file="T18_7_gblup_variances_all_3001_4000.rds")
+T18_7_gblup_variances_all_4001_5000=readRDS(file="T18_7_gblup_variances_all_4001_5000.rds")
+T18_7_gblup_variances_all_5001_6000=readRDS(file="T18_7_gblup_variances_all_5001_6000.rds")
+T18_7_gblup_variances_all_6001_7000=readRDS(file="T18_7_gblup_variances_all_6001_7000.rds")
+T18_7_gblup_variances_all_7001_8000=readRDS(file="T18_7_gblup_variances_all_7001_8000.rds")
+T18_7_gblup_variances_all_8001_9000=readRDS(file="T18_7_gblup_variances_all_8001_9000.rds")
+T18_7_gblup_variances_all_9001_10000=readRDS(file="T18_7_gblup_variances_all_9001_10000.rds")
+T18_7_gblup_variances_all_10001_11000=readRDS(file="T18_7_gblup_variances_all_10001_11000.rds")
+T18_7_gblup_variances_all_11001_12419=readRDS(file="T18_7_gblup_variances_all_11001_12419.rds")
+T18_7_gblup_variances_all=c(T18_7_gblup_variances_all_1_1000,T18_7_gblup_variances_all_1001_2000,T18_7_gblup_variances_all_2001_3000,T18_7_gblup_variances_all_3001_4000,T18_7_gblup_variances_all_4001_5000,T18_7_gblup_variances_all_5001_6000,T18_7_gblup_variances_all_6001_7000,T18_7_gblup_variances_all_7001_8000,T18_7_gblup_variances_all_8001_9000,T18_7_gblup_variances_all_9001_10000,T18_7_gblup_variances_all_10001_11000,T18_7_gblup_variances_all_11001_12419)
+
+saveRDS(T18_7_gblup_prediction_all,"T18_7_gblup_prediction_all.rds")
+saveRDS(T18_7_gblup_variances_all,"T18_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_7_gfblup_prediction_all_1_1000=readRDS(file="T18_7_gfblup_prediction_all_1_1000.rds")
+T18_7_gfblup_prediction_all_1001_2000=readRDS(file="T18_7_gfblup_prediction_all_1001_2000.rds")
+T18_7_gfblup_prediction_all_2001_3000=readRDS(file="T18_7_gfblup_prediction_all_2001_3000.rds")
+T18_7_gfblup_prediction_all_3001_4000=readRDS(file="T18_7_gfblup_prediction_all_3001_4000.rds")
+T18_7_gfblup_prediction_all_4001_5000=readRDS(file="T18_7_gfblup_prediction_all_4001_5000.rds")
+T18_7_gfblup_prediction_all_5001_6000=readRDS(file="T18_7_gfblup_prediction_all_5001_6000.rds")
+T18_7_gfblup_prediction_all_6001_7000=readRDS(file="T18_7_gfblup_prediction_all_6001_7000.rds")
+T18_7_gfblup_prediction_all_7001_8000=readRDS(file="T18_7_gfblup_prediction_all_7001_8000.rds")
+T18_7_gfblup_prediction_all_8001_9000=readRDS(file="T18_7_gfblup_prediction_all_8001_9000.rds")
+T18_7_gfblup_prediction_all_9001_10000=readRDS(file="T18_7_gfblup_prediction_all_9001_10000.rds")
+T18_7_gfblup_prediction_all_10001_11000=readRDS(file="T18_7_gfblup_prediction_all_10001_11000.rds")
+T18_7_gfblup_prediction_all_11001_12419=readRDS(file="T18_7_gfblup_prediction_all_11001_12419.rds")
+
+T18_7_gfblup_variances_all_1_1000=readRDS(file="T18_7_gfblup_variances_all_1_1000.rds")
+T18_7_gfblup_variances_all_1001_2000=readRDS(file="T18_7_gfblup_variances_all_1001_2000.rds")
+T18_7_gfblup_variances_all_2001_3000=readRDS(file="T18_7_gfblup_variances_all_2001_3000.rds")
+T18_7_gfblup_variances_all_3001_4000=readRDS(file="T18_7_gfblup_variances_all_3001_4000.rds")
+T18_7_gfblup_variances_all_4001_5000=readRDS(file="T18_7_gfblup_variances_all_4001_5000.rds")
+T18_7_gfblup_variances_all_5001_6000=readRDS(file="T18_7_gfblup_variances_all_5001_6000.rds")
+T18_7_gfblup_variances_all_6001_7000=readRDS(file="T18_7_gfblup_variances_all_6001_7000.rds")
+T18_7_gfblup_variances_all_7001_8000=readRDS(file="T18_7_gfblup_variances_all_7001_8000.rds")
+T18_7_gfblup_variances_all_8001_9000=readRDS(file="T18_7_gfblup_variances_all_8001_9000.rds")
+T18_7_gfblup_variances_all_9001_10000=readRDS(file="T18_7_gfblup_variances_all_9001_10000.rds")
+T18_7_gfblup_variances_all_10001_11000=readRDS(file="T18_7_gfblup_variances_all_10001_11000.rds")
+T18_7_gfblup_variances_all_11001_12419=readRDS(file="T18_7_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T18_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_7_gfblup_variances_all=rep(list(list()),cycles)
+T18_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_1_1000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_1001_2000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_2001_3000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_3001_4000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_4001_5000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_5001_6000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_6001_7000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_7001_8000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_8001_9000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_9001_10000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_10001_11000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_11001_12419[[r]])
+
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_1_1000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_1001_2000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_2001_3000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_3001_4000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_4001_5000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_5001_6000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_6001_7000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_7001_8000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_8001_9000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_9001_10000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_10001_11000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T18_7_gfblup_prediction_all,"T18_7_gfblup_prediction_all.rds")
+saveRDS(T18_7_gfblup_variances_all,"T18_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_8_gblup_prediction_all_1_1000=readRDS(file="T18_8_gblup_prediction_all_1_1000.rds")
+T18_8_gblup_prediction_all_1001_2000=readRDS(file="T18_8_gblup_prediction_all_1001_2000.rds")
+T18_8_gblup_prediction_all_2001_3000=readRDS(file="T18_8_gblup_prediction_all_2001_3000.rds")
+T18_8_gblup_prediction_all_3001_4000=readRDS(file="T18_8_gblup_prediction_all_3001_4000.rds")
+T18_8_gblup_prediction_all_4001_5000=readRDS(file="T18_8_gblup_prediction_all_4001_5000.rds")
+T18_8_gblup_prediction_all_5001_6000=readRDS(file="T18_8_gblup_prediction_all_5001_6000.rds")
+T18_8_gblup_prediction_all_6001_7000=readRDS(file="T18_8_gblup_prediction_all_6001_7000.rds")
+T18_8_gblup_prediction_all_7001_8000=readRDS(file="T18_8_gblup_prediction_all_7001_8000.rds")
+T18_8_gblup_prediction_all_8001_9000=readRDS(file="T18_8_gblup_prediction_all_8001_9000.rds")
+T18_8_gblup_prediction_all_9001_10000=readRDS(file="T18_8_gblup_prediction_all_9001_10000.rds")
+T18_8_gblup_prediction_all_10001_11000=readRDS(file="T18_8_gblup_prediction_all_10001_11000.rds")
+T18_8_gblup_prediction_all_11001_12419=readRDS(file="T18_8_gblup_prediction_all_11001_12419.rds")
+T18_8_gblup_prediction_all=c(T18_8_gblup_prediction_all_1_1000,T18_8_gblup_prediction_all_1001_2000,T18_8_gblup_prediction_all_2001_3000,T18_8_gblup_prediction_all_3001_4000,T18_8_gblup_prediction_all_4001_5000,T18_8_gblup_prediction_all_5001_6000,T18_8_gblup_prediction_all_6001_7000,T18_8_gblup_prediction_all_7001_8000,T18_8_gblup_prediction_all_8001_9000,T18_8_gblup_prediction_all_9001_10000,T18_8_gblup_prediction_all_10001_11000,T18_8_gblup_prediction_all_11001_12419)
+
+T18_8_gblup_variances_all_1_1000=readRDS(file="T18_8_gblup_variances_all_1_1000.rds")
+T18_8_gblup_variances_all_1001_2000=readRDS(file="T18_8_gblup_variances_all_1001_2000.rds")
+T18_8_gblup_variances_all_2001_3000=readRDS(file="T18_8_gblup_variances_all_2001_3000.rds")
+T18_8_gblup_variances_all_3001_4000=readRDS(file="T18_8_gblup_variances_all_3001_4000.rds")
+T18_8_gblup_variances_all_4001_5000=readRDS(file="T18_8_gblup_variances_all_4001_5000.rds")
+T18_8_gblup_variances_all_5001_6000=readRDS(file="T18_8_gblup_variances_all_5001_6000.rds")
+T18_8_gblup_variances_all_6001_7000=readRDS(file="T18_8_gblup_variances_all_6001_7000.rds")
+T18_8_gblup_variances_all_7001_8000=readRDS(file="T18_8_gblup_variances_all_7001_8000.rds")
+T18_8_gblup_variances_all_8001_9000=readRDS(file="T18_8_gblup_variances_all_8001_9000.rds")
+T18_8_gblup_variances_all_9001_10000=readRDS(file="T18_8_gblup_variances_all_9001_10000.rds")
+T18_8_gblup_variances_all_10001_11000=readRDS(file="T18_8_gblup_variances_all_10001_11000.rds")
+T18_8_gblup_variances_all_11001_12419=readRDS(file="T18_8_gblup_variances_all_11001_12419.rds")
+T18_8_gblup_variances_all=c(T18_8_gblup_variances_all_1_1000,T18_8_gblup_variances_all_1001_2000,T18_8_gblup_variances_all_2001_3000,T18_8_gblup_variances_all_3001_4000,T18_8_gblup_variances_all_4001_5000,T18_8_gblup_variances_all_5001_6000,T18_8_gblup_variances_all_6001_7000,T18_8_gblup_variances_all_7001_8000,T18_8_gblup_variances_all_8001_9000,T18_8_gblup_variances_all_9001_10000,T18_8_gblup_variances_all_10001_11000,T18_8_gblup_variances_all_11001_12419)
+
+saveRDS(T18_8_gblup_prediction_all,"T18_8_gblup_prediction_all.rds")
+saveRDS(T18_8_gblup_variances_all,"T18_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_8_gfblup_prediction_all_1_1000=readRDS(file="T18_8_gfblup_prediction_all_1_1000.rds")
+T18_8_gfblup_prediction_all_1001_2000=readRDS(file="T18_8_gfblup_prediction_all_1001_2000.rds")
+T18_8_gfblup_prediction_all_2001_3000=readRDS(file="T18_8_gfblup_prediction_all_2001_3000.rds")
+T18_8_gfblup_prediction_all_3001_4000=readRDS(file="T18_8_gfblup_prediction_all_3001_4000.rds")
+T18_8_gfblup_prediction_all_4001_5000=readRDS(file="T18_8_gfblup_prediction_all_4001_5000.rds")
+T18_8_gfblup_prediction_all_5001_6000=readRDS(file="T18_8_gfblup_prediction_all_5001_6000.rds")
+T18_8_gfblup_prediction_all_6001_7000=readRDS(file="T18_8_gfblup_prediction_all_6001_7000.rds")
+T18_8_gfblup_prediction_all_7001_8000=readRDS(file="T18_8_gfblup_prediction_all_7001_8000.rds")
+T18_8_gfblup_prediction_all_8001_9000=readRDS(file="T18_8_gfblup_prediction_all_8001_9000.rds")
+T18_8_gfblup_prediction_all_9001_10000=readRDS(file="T18_8_gfblup_prediction_all_9001_10000.rds")
+T18_8_gfblup_prediction_all_10001_11000=readRDS(file="T18_8_gfblup_prediction_all_10001_11000.rds")
+T18_8_gfblup_prediction_all_11001_12419=readRDS(file="T18_8_gfblup_prediction_all_11001_12419.rds")
+
+T18_8_gfblup_variances_all_1_1000=readRDS(file="T18_8_gfblup_variances_all_1_1000.rds")
+T18_8_gfblup_variances_all_1001_2000=readRDS(file="T18_8_gfblup_variances_all_1001_2000.rds")
+T18_8_gfblup_variances_all_2001_3000=readRDS(file="T18_8_gfblup_variances_all_2001_3000.rds")
+T18_8_gfblup_variances_all_3001_4000=readRDS(file="T18_8_gfblup_variances_all_3001_4000.rds")
+T18_8_gfblup_variances_all_4001_5000=readRDS(file="T18_8_gfblup_variances_all_4001_5000.rds")
+T18_8_gfblup_variances_all_5001_6000=readRDS(file="T18_8_gfblup_variances_all_5001_6000.rds")
+T18_8_gfblup_variances_all_6001_7000=readRDS(file="T18_8_gfblup_variances_all_6001_7000.rds")
+T18_8_gfblup_variances_all_7001_8000=readRDS(file="T18_8_gfblup_variances_all_7001_8000.rds")
+T18_8_gfblup_variances_all_8001_9000=readRDS(file="T18_8_gfblup_variances_all_8001_9000.rds")
+T18_8_gfblup_variances_all_9001_10000=readRDS(file="T18_8_gfblup_variances_all_9001_10000.rds")
+T18_8_gfblup_variances_all_10001_11000=readRDS(file="T18_8_gfblup_variances_all_10001_11000.rds")
+T18_8_gfblup_variances_all_11001_12419=readRDS(file="T18_8_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T18_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_8_gfblup_variances_all=rep(list(list()),cycles)
+T18_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_1_1000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_1001_2000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_2001_3000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_3001_4000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_4001_5000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_5001_6000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_6001_7000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_7001_8000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_8001_9000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_9001_10000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_10001_11000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_11001_12419[[r]])
+
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_1_1000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_1001_2000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_2001_3000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_3001_4000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_4001_5000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_5001_6000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_6001_7000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_7001_8000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_8001_9000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_9001_10000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_10001_11000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T18_8_gfblup_prediction_all,"T18_8_gfblup_prediction_all.rds")
+saveRDS(T18_8_gfblup_variances_all,"T18_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_1_gblup_prediction_all_1_1000=readRDS(file="T19_1_gblup_prediction_all_1_1000.rds")
+T19_1_gblup_prediction_all_1001_2000=readRDS(file="T19_1_gblup_prediction_all_1001_2000.rds")
+T19_1_gblup_prediction_all_2001_3000=readRDS(file="T19_1_gblup_prediction_all_2001_3000.rds")
+T19_1_gblup_prediction_all_3001_4000=readRDS(file="T19_1_gblup_prediction_all_3001_4000.rds")
+T19_1_gblup_prediction_all_4001_5000=readRDS(file="T19_1_gblup_prediction_all_4001_5000.rds")
+T19_1_gblup_prediction_all_5001_6000=readRDS(file="T19_1_gblup_prediction_all_5001_6000.rds")
+T19_1_gblup_prediction_all_6001_7000=readRDS(file="T19_1_gblup_prediction_all_6001_7000.rds")
+T19_1_gblup_prediction_all_7001_8000=readRDS(file="T19_1_gblup_prediction_all_7001_8000.rds")
+T19_1_gblup_prediction_all_8001_9000=readRDS(file="T19_1_gblup_prediction_all_8001_9000.rds")
+T19_1_gblup_prediction_all_9001_10000=readRDS(file="T19_1_gblup_prediction_all_9001_10000.rds")
+T19_1_gblup_prediction_all_10001_11000=readRDS(file="T19_1_gblup_prediction_all_10001_11000.rds")
+T19_1_gblup_prediction_all_11001_12419=readRDS(file="T19_1_gblup_prediction_all_11001_12419.rds")
+T19_1_gblup_prediction_all=c(T19_1_gblup_prediction_all_1_1000,T19_1_gblup_prediction_all_1001_2000,T19_1_gblup_prediction_all_2001_3000,T19_1_gblup_prediction_all_3001_4000,T19_1_gblup_prediction_all_4001_5000,T19_1_gblup_prediction_all_5001_6000,T19_1_gblup_prediction_all_6001_7000,T19_1_gblup_prediction_all_7001_8000,T19_1_gblup_prediction_all_8001_9000,T19_1_gblup_prediction_all_9001_10000,T19_1_gblup_prediction_all_10001_11000,T19_1_gblup_prediction_all_11001_12419)
+
+T19_1_gblup_variances_all_1_1000=readRDS(file="T19_1_gblup_variances_all_1_1000.rds")
+T19_1_gblup_variances_all_1001_2000=readRDS(file="T19_1_gblup_variances_all_1001_2000.rds")
+T19_1_gblup_variances_all_2001_3000=readRDS(file="T19_1_gblup_variances_all_2001_3000.rds")
+T19_1_gblup_variances_all_3001_4000=readRDS(file="T19_1_gblup_variances_all_3001_4000.rds")
+T19_1_gblup_variances_all_4001_5000=readRDS(file="T19_1_gblup_variances_all_4001_5000.rds")
+T19_1_gblup_variances_all_5001_6000=readRDS(file="T19_1_gblup_variances_all_5001_6000.rds")
+T19_1_gblup_variances_all_6001_7000=readRDS(file="T19_1_gblup_variances_all_6001_7000.rds")
+T19_1_gblup_variances_all_7001_8000=readRDS(file="T19_1_gblup_variances_all_7001_8000.rds")
+T19_1_gblup_variances_all_8001_9000=readRDS(file="T19_1_gblup_variances_all_8001_9000.rds")
+T19_1_gblup_variances_all_9001_10000=readRDS(file="T19_1_gblup_variances_all_9001_10000.rds")
+T19_1_gblup_variances_all_10001_11000=readRDS(file="T19_1_gblup_variances_all_10001_11000.rds")
+T19_1_gblup_variances_all_11001_12419=readRDS(file="T19_1_gblup_variances_all_11001_12419.rds")
+T19_1_gblup_variances_all=c(T19_1_gblup_variances_all_1_1000,T19_1_gblup_variances_all_1001_2000,T19_1_gblup_variances_all_2001_3000,T19_1_gblup_variances_all_3001_4000,T19_1_gblup_variances_all_4001_5000,T19_1_gblup_variances_all_5001_6000,T19_1_gblup_variances_all_6001_7000,T19_1_gblup_variances_all_7001_8000,T19_1_gblup_variances_all_8001_9000,T19_1_gblup_variances_all_9001_10000,T19_1_gblup_variances_all_10001_11000,T19_1_gblup_variances_all_11001_12419)
+
+saveRDS(T19_1_gblup_prediction_all,"T19_1_gblup_prediction_all.rds")
+saveRDS(T19_1_gblup_variances_all,"T19_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_1_gfblup_prediction_all_1_1000=readRDS(file="T19_1_gfblup_prediction_all_1_1000.rds")
+T19_1_gfblup_prediction_all_1001_2000=readRDS(file="T19_1_gfblup_prediction_all_1001_2000.rds")
+T19_1_gfblup_prediction_all_2001_3000=readRDS(file="T19_1_gfblup_prediction_all_2001_3000.rds")
+T19_1_gfblup_prediction_all_3001_4000=readRDS(file="T19_1_gfblup_prediction_all_3001_4000.rds")
+T19_1_gfblup_prediction_all_4001_5000=readRDS(file="T19_1_gfblup_prediction_all_4001_5000.rds")
+T19_1_gfblup_prediction_all_5001_6000=readRDS(file="T19_1_gfblup_prediction_all_5001_6000.rds")
+T19_1_gfblup_prediction_all_6001_7000=readRDS(file="T19_1_gfblup_prediction_all_6001_7000.rds")
+T19_1_gfblup_prediction_all_7001_8000=readRDS(file="T19_1_gfblup_prediction_all_7001_8000.rds")
+T19_1_gfblup_prediction_all_8001_9000=readRDS(file="T19_1_gfblup_prediction_all_8001_9000.rds")
+T19_1_gfblup_prediction_all_9001_10000=readRDS(file="T19_1_gfblup_prediction_all_9001_10000.rds")
+T19_1_gfblup_prediction_all_10001_11000=readRDS(file="T19_1_gfblup_prediction_all_10001_11000.rds")
+T19_1_gfblup_prediction_all_11001_12419=readRDS(file="T19_1_gfblup_prediction_all_11001_12419.rds")
+
+T19_1_gfblup_variances_all_1_1000=readRDS(file="T19_1_gfblup_variances_all_1_1000.rds")
+T19_1_gfblup_variances_all_1001_2000=readRDS(file="T19_1_gfblup_variances_all_1001_2000.rds")
+T19_1_gfblup_variances_all_2001_3000=readRDS(file="T19_1_gfblup_variances_all_2001_3000.rds")
+T19_1_gfblup_variances_all_3001_4000=readRDS(file="T19_1_gfblup_variances_all_3001_4000.rds")
+T19_1_gfblup_variances_all_4001_5000=readRDS(file="T19_1_gfblup_variances_all_4001_5000.rds")
+T19_1_gfblup_variances_all_5001_6000=readRDS(file="T19_1_gfblup_variances_all_5001_6000.rds")
+T19_1_gfblup_variances_all_6001_7000=readRDS(file="T19_1_gfblup_variances_all_6001_7000.rds")
+T19_1_gfblup_variances_all_7001_8000=readRDS(file="T19_1_gfblup_variances_all_7001_8000.rds")
+T19_1_gfblup_variances_all_8001_9000=readRDS(file="T19_1_gfblup_variances_all_8001_9000.rds")
+T19_1_gfblup_variances_all_9001_10000=readRDS(file="T19_1_gfblup_variances_all_9001_10000.rds")
+T19_1_gfblup_variances_all_10001_11000=readRDS(file="T19_1_gfblup_variances_all_10001_11000.rds")
+T19_1_gfblup_variances_all_11001_12419=readRDS(file="T19_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T19_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_1_gfblup_variances_all=rep(list(list()),cycles)
+T19_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_1_1000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_1001_2000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_2001_3000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_3001_4000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_4001_5000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_5001_6000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_6001_7000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_7001_8000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_8001_9000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_9001_10000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_10001_11000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_11001_12419[[r]])
+
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_1_1000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_1001_2000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_2001_3000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_3001_4000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_4001_5000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_5001_6000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_6001_7000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_7001_8000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_8001_9000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_9001_10000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_10001_11000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T19_1_gfblup_prediction_all,"T19_1_gfblup_prediction_all.rds")
+saveRDS(T19_1_gfblup_variances_all,"T19_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_2_gblup_prediction_all_1_1000=readRDS(file="T19_2_gblup_prediction_all_1_1000.rds")
+T19_2_gblup_prediction_all_1001_2000=readRDS(file="T19_2_gblup_prediction_all_1001_2000.rds")
+T19_2_gblup_prediction_all_2001_3000=readRDS(file="T19_2_gblup_prediction_all_2001_3000.rds")
+T19_2_gblup_prediction_all_3001_4000=readRDS(file="T19_2_gblup_prediction_all_3001_4000.rds")
+T19_2_gblup_prediction_all_4001_5000=readRDS(file="T19_2_gblup_prediction_all_4001_5000.rds")
+T19_2_gblup_prediction_all_5001_6000=readRDS(file="T19_2_gblup_prediction_all_5001_6000.rds")
+T19_2_gblup_prediction_all_6001_7000=readRDS(file="T19_2_gblup_prediction_all_6001_7000.rds")
+T19_2_gblup_prediction_all_7001_8000=readRDS(file="T19_2_gblup_prediction_all_7001_8000.rds")
+T19_2_gblup_prediction_all_8001_9000=readRDS(file="T19_2_gblup_prediction_all_8001_9000.rds")
+T19_2_gblup_prediction_all_9001_10000=readRDS(file="T19_2_gblup_prediction_all_9001_10000.rds")
+T19_2_gblup_prediction_all_10001_11000=readRDS(file="T19_2_gblup_prediction_all_10001_11000.rds")
+T19_2_gblup_prediction_all_11001_12419=readRDS(file="T19_2_gblup_prediction_all_11001_12419.rds")
+T19_2_gblup_prediction_all=c(T19_2_gblup_prediction_all_1_1000,T19_2_gblup_prediction_all_1001_2000,T19_2_gblup_prediction_all_2001_3000,T19_2_gblup_prediction_all_3001_4000,T19_2_gblup_prediction_all_4001_5000,T19_2_gblup_prediction_all_5001_6000,T19_2_gblup_prediction_all_6001_7000,T19_2_gblup_prediction_all_7001_8000,T19_2_gblup_prediction_all_8001_9000,T19_2_gblup_prediction_all_9001_10000,T19_2_gblup_prediction_all_10001_11000,T19_2_gblup_prediction_all_11001_12419)
+
+T19_2_gblup_variances_all_1_1000=readRDS(file="T19_2_gblup_variances_all_1_1000.rds")
+T19_2_gblup_variances_all_1001_2000=readRDS(file="T19_2_gblup_variances_all_1001_2000.rds")
+T19_2_gblup_variances_all_2001_3000=readRDS(file="T19_2_gblup_variances_all_2001_3000.rds")
+T19_2_gblup_variances_all_3001_4000=readRDS(file="T19_2_gblup_variances_all_3001_4000.rds")
+T19_2_gblup_variances_all_4001_5000=readRDS(file="T19_2_gblup_variances_all_4001_5000.rds")
+T19_2_gblup_variances_all_5001_6000=readRDS(file="T19_2_gblup_variances_all_5001_6000.rds")
+T19_2_gblup_variances_all_6001_7000=readRDS(file="T19_2_gblup_variances_all_6001_7000.rds")
+T19_2_gblup_variances_all_7001_8000=readRDS(file="T19_2_gblup_variances_all_7001_8000.rds")
+T19_2_gblup_variances_all_8001_9000=readRDS(file="T19_2_gblup_variances_all_8001_9000.rds")
+T19_2_gblup_variances_all_9001_10000=readRDS(file="T19_2_gblup_variances_all_9001_10000.rds")
+T19_2_gblup_variances_all_10001_11000=readRDS(file="T19_2_gblup_variances_all_10001_11000.rds")
+T19_2_gblup_variances_all_11001_12419=readRDS(file="T19_2_gblup_variances_all_11001_12419.rds")
+T19_2_gblup_variances_all=c(T19_2_gblup_variances_all_1_1000,T19_2_gblup_variances_all_1001_2000,T19_2_gblup_variances_all_2001_3000,T19_2_gblup_variances_all_3001_4000,T19_2_gblup_variances_all_4001_5000,T19_2_gblup_variances_all_5001_6000,T19_2_gblup_variances_all_6001_7000,T19_2_gblup_variances_all_7001_8000,T19_2_gblup_variances_all_8001_9000,T19_2_gblup_variances_all_9001_10000,T19_2_gblup_variances_all_10001_11000,T19_2_gblup_variances_all_11001_12419)
+
+saveRDS(T19_2_gblup_prediction_all,"T19_2_gblup_prediction_all.rds")
+saveRDS(T19_2_gblup_variances_all,"T19_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_2_gfblup_prediction_all_1_1000=readRDS(file="T19_2_gfblup_prediction_all_1_1000.rds")
+T19_2_gfblup_prediction_all_1001_2000=readRDS(file="T19_2_gfblup_prediction_all_1001_2000.rds")
+T19_2_gfblup_prediction_all_2001_3000=readRDS(file="T19_2_gfblup_prediction_all_2001_3000.rds")
+T19_2_gfblup_prediction_all_3001_4000=readRDS(file="T19_2_gfblup_prediction_all_3001_4000.rds")
+T19_2_gfblup_prediction_all_4001_5000=readRDS(file="T19_2_gfblup_prediction_all_4001_5000.rds")
+T19_2_gfblup_prediction_all_5001_6000=readRDS(file="T19_2_gfblup_prediction_all_5001_6000.rds")
+T19_2_gfblup_prediction_all_6001_7000=readRDS(file="T19_2_gfblup_prediction_all_6001_7000.rds")
+T19_2_gfblup_prediction_all_7001_8000=readRDS(file="T19_2_gfblup_prediction_all_7001_8000.rds")
+T19_2_gfblup_prediction_all_8001_9000=readRDS(file="T19_2_gfblup_prediction_all_8001_9000.rds")
+T19_2_gfblup_prediction_all_9001_10000=readRDS(file="T19_2_gfblup_prediction_all_9001_10000.rds")
+T19_2_gfblup_prediction_all_10001_11000=readRDS(file="T19_2_gfblup_prediction_all_10001_11000.rds")
+T19_2_gfblup_prediction_all_11001_12419=readRDS(file="T19_2_gfblup_prediction_all_11001_12419.rds")
+
+T19_2_gfblup_variances_all_1_1000=readRDS(file="T19_2_gfblup_variances_all_1_1000.rds")
+T19_2_gfblup_variances_all_1001_2000=readRDS(file="T19_2_gfblup_variances_all_1001_2000.rds")
+T19_2_gfblup_variances_all_2001_3000=readRDS(file="T19_2_gfblup_variances_all_2001_3000.rds")
+T19_2_gfblup_variances_all_3001_4000=readRDS(file="T19_2_gfblup_variances_all_3001_4000.rds")
+T19_2_gfblup_variances_all_4001_5000=readRDS(file="T19_2_gfblup_variances_all_4001_5000.rds")
+T19_2_gfblup_variances_all_5001_6000=readRDS(file="T19_2_gfblup_variances_all_5001_6000.rds")
+T19_2_gfblup_variances_all_6001_7000=readRDS(file="T19_2_gfblup_variances_all_6001_7000.rds")
+T19_2_gfblup_variances_all_7001_8000=readRDS(file="T19_2_gfblup_variances_all_7001_8000.rds")
+T19_2_gfblup_variances_all_8001_9000=readRDS(file="T19_2_gfblup_variances_all_8001_9000.rds")
+T19_2_gfblup_variances_all_9001_10000=readRDS(file="T19_2_gfblup_variances_all_9001_10000.rds")
+T19_2_gfblup_variances_all_10001_11000=readRDS(file="T19_2_gfblup_variances_all_10001_11000.rds")
+T19_2_gfblup_variances_all_11001_12419=readRDS(file="T19_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T19_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_2_gfblup_variances_all=rep(list(list()),cycles)
+T19_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_1_1000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_1001_2000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_2001_3000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_3001_4000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_4001_5000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_5001_6000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_6001_7000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_7001_8000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_8001_9000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_9001_10000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_10001_11000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_11001_12419[[r]])
+
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_1_1000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_1001_2000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_2001_3000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_3001_4000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_4001_5000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_5001_6000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_6001_7000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_7001_8000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_8001_9000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_9001_10000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_10001_11000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T19_2_gfblup_prediction_all,"T19_2_gfblup_prediction_all.rds")
+saveRDS(T19_2_gfblup_variances_all,"T19_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_3_gblup_prediction_all_1_1000=readRDS(file="T19_3_gblup_prediction_all_1_1000.rds")
+T19_3_gblup_prediction_all_1001_2000=readRDS(file="T19_3_gblup_prediction_all_1001_2000.rds")
+T19_3_gblup_prediction_all_2001_3000=readRDS(file="T19_3_gblup_prediction_all_2001_3000.rds")
+T19_3_gblup_prediction_all_3001_4000=readRDS(file="T19_3_gblup_prediction_all_3001_4000.rds")
+T19_3_gblup_prediction_all_4001_5000=readRDS(file="T19_3_gblup_prediction_all_4001_5000.rds")
+T19_3_gblup_prediction_all_5001_6000=readRDS(file="T19_3_gblup_prediction_all_5001_6000.rds")
+T19_3_gblup_prediction_all_6001_7000=readRDS(file="T19_3_gblup_prediction_all_6001_7000.rds")
+T19_3_gblup_prediction_all_7001_8000=readRDS(file="T19_3_gblup_prediction_all_7001_8000.rds")
+T19_3_gblup_prediction_all_8001_9000=readRDS(file="T19_3_gblup_prediction_all_8001_9000.rds")
+T19_3_gblup_prediction_all_9001_10000=readRDS(file="T19_3_gblup_prediction_all_9001_10000.rds")
+T19_3_gblup_prediction_all_10001_11000=readRDS(file="T19_3_gblup_prediction_all_10001_11000.rds")
+T19_3_gblup_prediction_all_11001_12419=readRDS(file="T19_3_gblup_prediction_all_11001_12419.rds")
+T19_3_gblup_prediction_all=c(T19_3_gblup_prediction_all_1_1000,T19_3_gblup_prediction_all_1001_2000,T19_3_gblup_prediction_all_2001_3000,T19_3_gblup_prediction_all_3001_4000,T19_3_gblup_prediction_all_4001_5000,T19_3_gblup_prediction_all_5001_6000,T19_3_gblup_prediction_all_6001_7000,T19_3_gblup_prediction_all_7001_8000,T19_3_gblup_prediction_all_8001_9000,T19_3_gblup_prediction_all_9001_10000,T19_3_gblup_prediction_all_10001_11000,T19_3_gblup_prediction_all_11001_12419)
+
+T19_3_gblup_variances_all_1_1000=readRDS(file="T19_3_gblup_variances_all_1_1000.rds")
+T19_3_gblup_variances_all_1001_2000=readRDS(file="T19_3_gblup_variances_all_1001_2000.rds")
+T19_3_gblup_variances_all_2001_3000=readRDS(file="T19_3_gblup_variances_all_2001_3000.rds")
+T19_3_gblup_variances_all_3001_4000=readRDS(file="T19_3_gblup_variances_all_3001_4000.rds")
+T19_3_gblup_variances_all_4001_5000=readRDS(file="T19_3_gblup_variances_all_4001_5000.rds")
+T19_3_gblup_variances_all_5001_6000=readRDS(file="T19_3_gblup_variances_all_5001_6000.rds")
+T19_3_gblup_variances_all_6001_7000=readRDS(file="T19_3_gblup_variances_all_6001_7000.rds")
+T19_3_gblup_variances_all_7001_8000=readRDS(file="T19_3_gblup_variances_all_7001_8000.rds")
+T19_3_gblup_variances_all_8001_9000=readRDS(file="T19_3_gblup_variances_all_8001_9000.rds")
+T19_3_gblup_variances_all_9001_10000=readRDS(file="T19_3_gblup_variances_all_9001_10000.rds")
+T19_3_gblup_variances_all_10001_11000=readRDS(file="T19_3_gblup_variances_all_10001_11000.rds")
+T19_3_gblup_variances_all_11001_12419=readRDS(file="T19_3_gblup_variances_all_11001_12419.rds")
+T19_3_gblup_variances_all=c(T19_3_gblup_variances_all_1_1000,T19_3_gblup_variances_all_1001_2000,T19_3_gblup_variances_all_2001_3000,T19_3_gblup_variances_all_3001_4000,T19_3_gblup_variances_all_4001_5000,T19_3_gblup_variances_all_5001_6000,T19_3_gblup_variances_all_6001_7000,T19_3_gblup_variances_all_7001_8000,T19_3_gblup_variances_all_8001_9000,T19_3_gblup_variances_all_9001_10000,T19_3_gblup_variances_all_10001_11000,T19_3_gblup_variances_all_11001_12419)
+
+saveRDS(T19_3_gblup_prediction_all,"T19_3_gblup_prediction_all.rds")
+saveRDS(T19_3_gblup_variances_all,"T19_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_3_gfblup_prediction_all_1_1000=readRDS(file="T19_3_gfblup_prediction_all_1_1000.rds")
+T19_3_gfblup_prediction_all_1001_2000=readRDS(file="T19_3_gfblup_prediction_all_1001_2000.rds")
+T19_3_gfblup_prediction_all_2001_3000=readRDS(file="T19_3_gfblup_prediction_all_2001_3000.rds")
+T19_3_gfblup_prediction_all_3001_4000=readRDS(file="T19_3_gfblup_prediction_all_3001_4000.rds")
+T19_3_gfblup_prediction_all_4001_5000=readRDS(file="T19_3_gfblup_prediction_all_4001_5000.rds")
+T19_3_gfblup_prediction_all_5001_6000=readRDS(file="T19_3_gfblup_prediction_all_5001_6000.rds")
+T19_3_gfblup_prediction_all_6001_7000=readRDS(file="T19_3_gfblup_prediction_all_6001_7000.rds")
+T19_3_gfblup_prediction_all_7001_8000=readRDS(file="T19_3_gfblup_prediction_all_7001_8000.rds")
+T19_3_gfblup_prediction_all_8001_9000=readRDS(file="T19_3_gfblup_prediction_all_8001_9000.rds")
+T19_3_gfblup_prediction_all_9001_10000=readRDS(file="T19_3_gfblup_prediction_all_9001_10000.rds")
+T19_3_gfblup_prediction_all_10001_11000=readRDS(file="T19_3_gfblup_prediction_all_10001_11000.rds")
+T19_3_gfblup_prediction_all_11001_12419=readRDS(file="T19_3_gfblup_prediction_all_11001_12419.rds")
+
+T19_3_gfblup_variances_all_1_1000=readRDS(file="T19_3_gfblup_variances_all_1_1000.rds")
+T19_3_gfblup_variances_all_1001_2000=readRDS(file="T19_3_gfblup_variances_all_1001_2000.rds")
+T19_3_gfblup_variances_all_2001_3000=readRDS(file="T19_3_gfblup_variances_all_2001_3000.rds")
+T19_3_gfblup_variances_all_3001_4000=readRDS(file="T19_3_gfblup_variances_all_3001_4000.rds")
+T19_3_gfblup_variances_all_4001_5000=readRDS(file="T19_3_gfblup_variances_all_4001_5000.rds")
+T19_3_gfblup_variances_all_5001_6000=readRDS(file="T19_3_gfblup_variances_all_5001_6000.rds")
+T19_3_gfblup_variances_all_6001_7000=readRDS(file="T19_3_gfblup_variances_all_6001_7000.rds")
+T19_3_gfblup_variances_all_7001_8000=readRDS(file="T19_3_gfblup_variances_all_7001_8000.rds")
+T19_3_gfblup_variances_all_8001_9000=readRDS(file="T19_3_gfblup_variances_all_8001_9000.rds")
+T19_3_gfblup_variances_all_9001_10000=readRDS(file="T19_3_gfblup_variances_all_9001_10000.rds")
+T19_3_gfblup_variances_all_10001_11000=readRDS(file="T19_3_gfblup_variances_all_10001_11000.rds")
+T19_3_gfblup_variances_all_11001_12419=readRDS(file="T19_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T19_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_3_gfblup_variances_all=rep(list(list()),cycles)
+T19_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_1_1000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_1001_2000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_2001_3000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_3001_4000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_4001_5000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_5001_6000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_6001_7000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_7001_8000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_8001_9000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_9001_10000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_10001_11000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_11001_12419[[r]])
+
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_1_1000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_1001_2000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_2001_3000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_3001_4000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_4001_5000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_5001_6000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_6001_7000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_7001_8000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_8001_9000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_9001_10000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_10001_11000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T19_3_gfblup_prediction_all,"T19_3_gfblup_prediction_all.rds")
+saveRDS(T19_3_gfblup_variances_all,"T19_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_4_gblup_prediction_all_1_1000=readRDS(file="T19_4_gblup_prediction_all_1_1000.rds")
+T19_4_gblup_prediction_all_1001_2000=readRDS(file="T19_4_gblup_prediction_all_1001_2000.rds")
+T19_4_gblup_prediction_all_2001_3000=readRDS(file="T19_4_gblup_prediction_all_2001_3000.rds")
+T19_4_gblup_prediction_all_3001_4000=readRDS(file="T19_4_gblup_prediction_all_3001_4000.rds")
+T19_4_gblup_prediction_all_4001_5000=readRDS(file="T19_4_gblup_prediction_all_4001_5000.rds")
+T19_4_gblup_prediction_all_5001_6000=readRDS(file="T19_4_gblup_prediction_all_5001_6000.rds")
+T19_4_gblup_prediction_all_6001_7000=readRDS(file="T19_4_gblup_prediction_all_6001_7000.rds")
+T19_4_gblup_prediction_all_7001_8000=readRDS(file="T19_4_gblup_prediction_all_7001_8000.rds")
+T19_4_gblup_prediction_all_8001_9000=readRDS(file="T19_4_gblup_prediction_all_8001_9000.rds")
+T19_4_gblup_prediction_all_9001_10000=readRDS(file="T19_4_gblup_prediction_all_9001_10000.rds")
+T19_4_gblup_prediction_all_10001_11000=readRDS(file="T19_4_gblup_prediction_all_10001_11000.rds")
+T19_4_gblup_prediction_all_11001_12419=readRDS(file="T19_4_gblup_prediction_all_11001_12419.rds")
+T19_4_gblup_prediction_all=c(T19_4_gblup_prediction_all_1_1000,T19_4_gblup_prediction_all_1001_2000,T19_4_gblup_prediction_all_2001_3000,T19_4_gblup_prediction_all_3001_4000,T19_4_gblup_prediction_all_4001_5000,T19_4_gblup_prediction_all_5001_6000,T19_4_gblup_prediction_all_6001_7000,T19_4_gblup_prediction_all_7001_8000,T19_4_gblup_prediction_all_8001_9000,T19_4_gblup_prediction_all_9001_10000,T19_4_gblup_prediction_all_10001_11000,T19_4_gblup_prediction_all_11001_12419)
+
+T19_4_gblup_variances_all_1_1000=readRDS(file="T19_4_gblup_variances_all_1_1000.rds")
+T19_4_gblup_variances_all_1001_2000=readRDS(file="T19_4_gblup_variances_all_1001_2000.rds")
+T19_4_gblup_variances_all_2001_3000=readRDS(file="T19_4_gblup_variances_all_2001_3000.rds")
+T19_4_gblup_variances_all_3001_4000=readRDS(file="T19_4_gblup_variances_all_3001_4000.rds")
+T19_4_gblup_variances_all_4001_5000=readRDS(file="T19_4_gblup_variances_all_4001_5000.rds")
+T19_4_gblup_variances_all_5001_6000=readRDS(file="T19_4_gblup_variances_all_5001_6000.rds")
+T19_4_gblup_variances_all_6001_7000=readRDS(file="T19_4_gblup_variances_all_6001_7000.rds")
+T19_4_gblup_variances_all_7001_8000=readRDS(file="T19_4_gblup_variances_all_7001_8000.rds")
+T19_4_gblup_variances_all_8001_9000=readRDS(file="T19_4_gblup_variances_all_8001_9000.rds")
+T19_4_gblup_variances_all_9001_10000=readRDS(file="T19_4_gblup_variances_all_9001_10000.rds")
+T19_4_gblup_variances_all_10001_11000=readRDS(file="T19_4_gblup_variances_all_10001_11000.rds")
+T19_4_gblup_variances_all_11001_12419=readRDS(file="T19_4_gblup_variances_all_11001_12419.rds")
+T19_4_gblup_variances_all=c(T19_4_gblup_variances_all_1_1000,T19_4_gblup_variances_all_1001_2000,T19_4_gblup_variances_all_2001_3000,T19_4_gblup_variances_all_3001_4000,T19_4_gblup_variances_all_4001_5000,T19_4_gblup_variances_all_5001_6000,T19_4_gblup_variances_all_6001_7000,T19_4_gblup_variances_all_7001_8000,T19_4_gblup_variances_all_8001_9000,T19_4_gblup_variances_all_9001_10000,T19_4_gblup_variances_all_10001_11000,T19_4_gblup_variances_all_11001_12419)
+
+saveRDS(T19_4_gblup_prediction_all,"T19_4_gblup_prediction_all.rds")
+saveRDS(T19_4_gblup_variances_all,"T19_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_4_gfblup_prediction_all_1_1000=readRDS(file="T19_4_gfblup_prediction_all_1_1000.rds")
+T19_4_gfblup_prediction_all_1001_2000=readRDS(file="T19_4_gfblup_prediction_all_1001_2000.rds")
+T19_4_gfblup_prediction_all_2001_3000=readRDS(file="T19_4_gfblup_prediction_all_2001_3000.rds")
+T19_4_gfblup_prediction_all_3001_4000=readRDS(file="T19_4_gfblup_prediction_all_3001_4000.rds")
+T19_4_gfblup_prediction_all_4001_5000=readRDS(file="T19_4_gfblup_prediction_all_4001_5000.rds")
+T19_4_gfblup_prediction_all_5001_6000=readRDS(file="T19_4_gfblup_prediction_all_5001_6000.rds")
+T19_4_gfblup_prediction_all_6001_7000=readRDS(file="T19_4_gfblup_prediction_all_6001_7000.rds")
+T19_4_gfblup_prediction_all_7001_8000=readRDS(file="T19_4_gfblup_prediction_all_7001_8000.rds")
+T19_4_gfblup_prediction_all_8001_9000=readRDS(file="T19_4_gfblup_prediction_all_8001_9000.rds")
+T19_4_gfblup_prediction_all_9001_10000=readRDS(file="T19_4_gfblup_prediction_all_9001_10000.rds")
+T19_4_gfblup_prediction_all_10001_11000=readRDS(file="T19_4_gfblup_prediction_all_10001_11000.rds")
+T19_4_gfblup_prediction_all_11001_12419=readRDS(file="T19_4_gfblup_prediction_all_11001_12419.rds")
+
+T19_4_gfblup_variances_all_1_1000=readRDS(file="T19_4_gfblup_variances_all_1_1000.rds")
+T19_4_gfblup_variances_all_1001_2000=readRDS(file="T19_4_gfblup_variances_all_1001_2000.rds")
+T19_4_gfblup_variances_all_2001_3000=readRDS(file="T19_4_gfblup_variances_all_2001_3000.rds")
+T19_4_gfblup_variances_all_3001_4000=readRDS(file="T19_4_gfblup_variances_all_3001_4000.rds")
+T19_4_gfblup_variances_all_4001_5000=readRDS(file="T19_4_gfblup_variances_all_4001_5000.rds")
+T19_4_gfblup_variances_all_5001_6000=readRDS(file="T19_4_gfblup_variances_all_5001_6000.rds")
+T19_4_gfblup_variances_all_6001_7000=readRDS(file="T19_4_gfblup_variances_all_6001_7000.rds")
+T19_4_gfblup_variances_all_7001_8000=readRDS(file="T19_4_gfblup_variances_all_7001_8000.rds")
+T19_4_gfblup_variances_all_8001_9000=readRDS(file="T19_4_gfblup_variances_all_8001_9000.rds")
+T19_4_gfblup_variances_all_9001_10000=readRDS(file="T19_4_gfblup_variances_all_9001_10000.rds")
+T19_4_gfblup_variances_all_10001_11000=readRDS(file="T19_4_gfblup_variances_all_10001_11000.rds")
+T19_4_gfblup_variances_all_11001_12419=readRDS(file="T19_4_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T19_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_4_gfblup_variances_all=rep(list(list()),cycles)
+T19_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_1_1000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_1001_2000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_2001_3000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_3001_4000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_4001_5000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_5001_6000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_6001_7000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_7001_8000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_8001_9000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_9001_10000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_10001_11000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_11001_12419[[r]])
+
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_1_1000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_1001_2000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_2001_3000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_3001_4000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_4001_5000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_5001_6000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_6001_7000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_7001_8000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_8001_9000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_9001_10000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_10001_11000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T19_4_gfblup_prediction_all,"T19_4_gfblup_prediction_all.rds")
+saveRDS(T19_4_gfblup_variances_all,"T19_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_5_gblup_prediction_all_1_1000=readRDS(file="T19_5_gblup_prediction_all_1_1000.rds")
+T19_5_gblup_prediction_all_1001_2000=readRDS(file="T19_5_gblup_prediction_all_1001_2000.rds")
+T19_5_gblup_prediction_all_2001_3000=readRDS(file="T19_5_gblup_prediction_all_2001_3000.rds")
+T19_5_gblup_prediction_all_3001_4000=readRDS(file="T19_5_gblup_prediction_all_3001_4000.rds")
+T19_5_gblup_prediction_all_4001_5000=readRDS(file="T19_5_gblup_prediction_all_4001_5000.rds")
+T19_5_gblup_prediction_all_5001_6000=readRDS(file="T19_5_gblup_prediction_all_5001_6000.rds")
+T19_5_gblup_prediction_all_6001_7000=readRDS(file="T19_5_gblup_prediction_all_6001_7000.rds")
+T19_5_gblup_prediction_all_7001_8000=readRDS(file="T19_5_gblup_prediction_all_7001_8000.rds")
+T19_5_gblup_prediction_all_8001_9000=readRDS(file="T19_5_gblup_prediction_all_8001_9000.rds")
+T19_5_gblup_prediction_all_9001_10000=readRDS(file="T19_5_gblup_prediction_all_9001_10000.rds")
+T19_5_gblup_prediction_all_10001_11000=readRDS(file="T19_5_gblup_prediction_all_10001_11000.rds")
+T19_5_gblup_prediction_all_11001_12419=readRDS(file="T19_5_gblup_prediction_all_11001_12419.rds")
+T19_5_gblup_prediction_all=c(T19_5_gblup_prediction_all_1_1000,T19_5_gblup_prediction_all_1001_2000,T19_5_gblup_prediction_all_2001_3000,T19_5_gblup_prediction_all_3001_4000,T19_5_gblup_prediction_all_4001_5000,T19_5_gblup_prediction_all_5001_6000,T19_5_gblup_prediction_all_6001_7000,T19_5_gblup_prediction_all_7001_8000,T19_5_gblup_prediction_all_8001_9000,T19_5_gblup_prediction_all_9001_10000,T19_5_gblup_prediction_all_10001_11000,T19_5_gblup_prediction_all_11001_12419)
+
+T19_5_gblup_variances_all_1_1000=readRDS(file="T19_5_gblup_variances_all_1_1000.rds")
+T19_5_gblup_variances_all_1001_2000=readRDS(file="T19_5_gblup_variances_all_1001_2000.rds")
+T19_5_gblup_variances_all_2001_3000=readRDS(file="T19_5_gblup_variances_all_2001_3000.rds")
+T19_5_gblup_variances_all_3001_4000=readRDS(file="T19_5_gblup_variances_all_3001_4000.rds")
+T19_5_gblup_variances_all_4001_5000=readRDS(file="T19_5_gblup_variances_all_4001_5000.rds")
+T19_5_gblup_variances_all_5001_6000=readRDS(file="T19_5_gblup_variances_all_5001_6000.rds")
+T19_5_gblup_variances_all_6001_7000=readRDS(file="T19_5_gblup_variances_all_6001_7000.rds")
+T19_5_gblup_variances_all_7001_8000=readRDS(file="T19_5_gblup_variances_all_7001_8000.rds")
+T19_5_gblup_variances_all_8001_9000=readRDS(file="T19_5_gblup_variances_all_8001_9000.rds")
+T19_5_gblup_variances_all_9001_10000=readRDS(file="T19_5_gblup_variances_all_9001_10000.rds")
+T19_5_gblup_variances_all_10001_11000=readRDS(file="T19_5_gblup_variances_all_10001_11000.rds")
+T19_5_gblup_variances_all_11001_12419=readRDS(file="T19_5_gblup_variances_all_11001_12419.rds")
+T19_5_gblup_variances_all=c(T19_5_gblup_variances_all_1_1000,T19_5_gblup_variances_all_1001_2000,T19_5_gblup_variances_all_2001_3000,T19_5_gblup_variances_all_3001_4000,T19_5_gblup_variances_all_4001_5000,T19_5_gblup_variances_all_5001_6000,T19_5_gblup_variances_all_6001_7000,T19_5_gblup_variances_all_7001_8000,T19_5_gblup_variances_all_8001_9000,T19_5_gblup_variances_all_9001_10000,T19_5_gblup_variances_all_10001_11000,T19_5_gblup_variances_all_11001_12419)
+
+saveRDS(T19_5_gblup_prediction_all,"T19_5_gblup_prediction_all.rds")
+saveRDS(T19_5_gblup_variances_all,"T19_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_5_gfblup_prediction_all_1_1000=readRDS(file="T19_5_gfblup_prediction_all_1_1000.rds")
+T19_5_gfblup_prediction_all_1001_2000=readRDS(file="T19_5_gfblup_prediction_all_1001_2000.rds")
+T19_5_gfblup_prediction_all_2001_3000=readRDS(file="T19_5_gfblup_prediction_all_2001_3000.rds")
+T19_5_gfblup_prediction_all_3001_4000=readRDS(file="T19_5_gfblup_prediction_all_3001_4000.rds")
+T19_5_gfblup_prediction_all_4001_5000=readRDS(file="T19_5_gfblup_prediction_all_4001_5000.rds")
+T19_5_gfblup_prediction_all_5001_6000=readRDS(file="T19_5_gfblup_prediction_all_5001_6000.rds")
+T19_5_gfblup_prediction_all_6001_7000=readRDS(file="T19_5_gfblup_prediction_all_6001_7000.rds")
+T19_5_gfblup_prediction_all_7001_8000=readRDS(file="T19_5_gfblup_prediction_all_7001_8000.rds")
+T19_5_gfblup_prediction_all_8001_9000=readRDS(file="T19_5_gfblup_prediction_all_8001_9000.rds")
+T19_5_gfblup_prediction_all_9001_10000=readRDS(file="T19_5_gfblup_prediction_all_9001_10000.rds")
+T19_5_gfblup_prediction_all_10001_11000=readRDS(file="T19_5_gfblup_prediction_all_10001_11000.rds")
+T19_5_gfblup_prediction_all_11001_12419=readRDS(file="T19_5_gfblup_prediction_all_11001_12419.rds")
+
+T19_5_gfblup_variances_all_1_1000=readRDS(file="T19_5_gfblup_variances_all_1_1000.rds")
+T19_5_gfblup_variances_all_1001_2000=readRDS(file="T19_5_gfblup_variances_all_1001_2000.rds")
+T19_5_gfblup_variances_all_2001_3000=readRDS(file="T19_5_gfblup_variances_all_2001_3000.rds")
+T19_5_gfblup_variances_all_3001_4000=readRDS(file="T19_5_gfblup_variances_all_3001_4000.rds")
+T19_5_gfblup_variances_all_4001_5000=readRDS(file="T19_5_gfblup_variances_all_4001_5000.rds")
+T19_5_gfblup_variances_all_5001_6000=readRDS(file="T19_5_gfblup_variances_all_5001_6000.rds")
+T19_5_gfblup_variances_all_6001_7000=readRDS(file="T19_5_gfblup_variances_all_6001_7000.rds")
+T19_5_gfblup_variances_all_7001_8000=readRDS(file="T19_5_gfblup_variances_all_7001_8000.rds")
+T19_5_gfblup_variances_all_8001_9000=readRDS(file="T19_5_gfblup_variances_all_8001_9000.rds")
+T19_5_gfblup_variances_all_9001_10000=readRDS(file="T19_5_gfblup_variances_all_9001_10000.rds")
+T19_5_gfblup_variances_all_10001_11000=readRDS(file="T19_5_gfblup_variances_all_10001_11000.rds")
+T19_5_gfblup_variances_all_11001_12419=readRDS(file="T19_5_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T19_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_5_gfblup_variances_all=rep(list(list()),cycles)
+T19_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_1_1000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_1001_2000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_2001_3000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_3001_4000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_4001_5000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_5001_6000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_6001_7000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_7001_8000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_8001_9000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_9001_10000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_10001_11000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_11001_12419[[r]])
+
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_1_1000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_1001_2000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_2001_3000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_3001_4000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_4001_5000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_5001_6000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_6001_7000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_7001_8000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_8001_9000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_9001_10000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_10001_11000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T19_5_gfblup_prediction_all,"T19_5_gfblup_prediction_all.rds")
+saveRDS(T19_5_gfblup_variances_all,"T19_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_6_gblup_prediction_all_1_1000=readRDS(file="T19_6_gblup_prediction_all_1_1000.rds")
+T19_6_gblup_prediction_all_1001_2000=readRDS(file="T19_6_gblup_prediction_all_1001_2000.rds")
+T19_6_gblup_prediction_all_2001_3000=readRDS(file="T19_6_gblup_prediction_all_2001_3000.rds")
+T19_6_gblup_prediction_all_3001_4000=readRDS(file="T19_6_gblup_prediction_all_3001_4000.rds")
+T19_6_gblup_prediction_all_4001_5000=readRDS(file="T19_6_gblup_prediction_all_4001_5000.rds")
+T19_6_gblup_prediction_all_5001_6000=readRDS(file="T19_6_gblup_prediction_all_5001_6000.rds")
+T19_6_gblup_prediction_all_6001_7000=readRDS(file="T19_6_gblup_prediction_all_6001_7000.rds")
+T19_6_gblup_prediction_all_7001_8000=readRDS(file="T19_6_gblup_prediction_all_7001_8000.rds")
+T19_6_gblup_prediction_all_8001_9000=readRDS(file="T19_6_gblup_prediction_all_8001_9000.rds")
+T19_6_gblup_prediction_all_9001_10000=readRDS(file="T19_6_gblup_prediction_all_9001_10000.rds")
+T19_6_gblup_prediction_all_10001_11000=readRDS(file="T19_6_gblup_prediction_all_10001_11000.rds")
+T19_6_gblup_prediction_all_11001_12419=readRDS(file="T19_6_gblup_prediction_all_11001_12419.rds")
+T19_6_gblup_prediction_all=c(T19_6_gblup_prediction_all_1_1000,T19_6_gblup_prediction_all_1001_2000,T19_6_gblup_prediction_all_2001_3000,T19_6_gblup_prediction_all_3001_4000,T19_6_gblup_prediction_all_4001_5000,T19_6_gblup_prediction_all_5001_6000,T19_6_gblup_prediction_all_6001_7000,T19_6_gblup_prediction_all_7001_8000,T19_6_gblup_prediction_all_8001_9000,T19_6_gblup_prediction_all_9001_10000,T19_6_gblup_prediction_all_10001_11000,T19_6_gblup_prediction_all_11001_12419)
+
+T19_6_gblup_variances_all_1_1000=readRDS(file="T19_6_gblup_variances_all_1_1000.rds")
+T19_6_gblup_variances_all_1001_2000=readRDS(file="T19_6_gblup_variances_all_1001_2000.rds")
+T19_6_gblup_variances_all_2001_3000=readRDS(file="T19_6_gblup_variances_all_2001_3000.rds")
+T19_6_gblup_variances_all_3001_4000=readRDS(file="T19_6_gblup_variances_all_3001_4000.rds")
+T19_6_gblup_variances_all_4001_5000=readRDS(file="T19_6_gblup_variances_all_4001_5000.rds")
+T19_6_gblup_variances_all_5001_6000=readRDS(file="T19_6_gblup_variances_all_5001_6000.rds")
+T19_6_gblup_variances_all_6001_7000=readRDS(file="T19_6_gblup_variances_all_6001_7000.rds")
+T19_6_gblup_variances_all_7001_8000=readRDS(file="T19_6_gblup_variances_all_7001_8000.rds")
+T19_6_gblup_variances_all_8001_9000=readRDS(file="T19_6_gblup_variances_all_8001_9000.rds")
+T19_6_gblup_variances_all_9001_10000=readRDS(file="T19_6_gblup_variances_all_9001_10000.rds")
+T19_6_gblup_variances_all_10001_11000=readRDS(file="T19_6_gblup_variances_all_10001_11000.rds")
+T19_6_gblup_variances_all_11001_12419=readRDS(file="T19_6_gblup_variances_all_11001_12419.rds")
+T19_6_gblup_variances_all=c(T19_6_gblup_variances_all_1_1000,T19_6_gblup_variances_all_1001_2000,T19_6_gblup_variances_all_2001_3000,T19_6_gblup_variances_all_3001_4000,T19_6_gblup_variances_all_4001_5000,T19_6_gblup_variances_all_5001_6000,T19_6_gblup_variances_all_6001_7000,T19_6_gblup_variances_all_7001_8000,T19_6_gblup_variances_all_8001_9000,T19_6_gblup_variances_all_9001_10000,T19_6_gblup_variances_all_10001_11000,T19_6_gblup_variances_all_11001_12419)
+
+saveRDS(T19_6_gblup_prediction_all,"T19_6_gblup_prediction_all.rds")
+saveRDS(T19_6_gblup_variances_all,"T19_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_6_gfblup_prediction_all_1_1000=readRDS(file="T19_6_gfblup_prediction_all_1_1000.rds")
+T19_6_gfblup_prediction_all_1001_2000=readRDS(file="T19_6_gfblup_prediction_all_1001_2000.rds")
+T19_6_gfblup_prediction_all_2001_3000=readRDS(file="T19_6_gfblup_prediction_all_2001_3000.rds")
+T19_6_gfblup_prediction_all_3001_4000=readRDS(file="T19_6_gfblup_prediction_all_3001_4000.rds")
+T19_6_gfblup_prediction_all_4001_5000=readRDS(file="T19_6_gfblup_prediction_all_4001_5000.rds")
+T19_6_gfblup_prediction_all_5001_6000=readRDS(file="T19_6_gfblup_prediction_all_5001_6000.rds")
+T19_6_gfblup_prediction_all_6001_7000=readRDS(file="T19_6_gfblup_prediction_all_6001_7000.rds")
+T19_6_gfblup_prediction_all_7001_8000=readRDS(file="T19_6_gfblup_prediction_all_7001_8000.rds")
+T19_6_gfblup_prediction_all_8001_9000=readRDS(file="T19_6_gfblup_prediction_all_8001_9000.rds")
+T19_6_gfblup_prediction_all_9001_10000=readRDS(file="T19_6_gfblup_prediction_all_9001_10000.rds")
+T19_6_gfblup_prediction_all_10001_11000=readRDS(file="T19_6_gfblup_prediction_all_10001_11000.rds")
+T19_6_gfblup_prediction_all_11001_12419=readRDS(file="T19_6_gfblup_prediction_all_11001_12419.rds")
+
+T19_6_gfblup_variances_all_1_1000=readRDS(file="T19_6_gfblup_variances_all_1_1000.rds")
+T19_6_gfblup_variances_all_1001_2000=readRDS(file="T19_6_gfblup_variances_all_1001_2000.rds")
+T19_6_gfblup_variances_all_2001_3000=readRDS(file="T19_6_gfblup_variances_all_2001_3000.rds")
+T19_6_gfblup_variances_all_3001_4000=readRDS(file="T19_6_gfblup_variances_all_3001_4000.rds")
+T19_6_gfblup_variances_all_4001_5000=readRDS(file="T19_6_gfblup_variances_all_4001_5000.rds")
+T19_6_gfblup_variances_all_5001_6000=readRDS(file="T19_6_gfblup_variances_all_5001_6000.rds")
+T19_6_gfblup_variances_all_6001_7000=readRDS(file="T19_6_gfblup_variances_all_6001_7000.rds")
+T19_6_gfblup_variances_all_7001_8000=readRDS(file="T19_6_gfblup_variances_all_7001_8000.rds")
+T19_6_gfblup_variances_all_8001_9000=readRDS(file="T19_6_gfblup_variances_all_8001_9000.rds")
+T19_6_gfblup_variances_all_9001_10000=readRDS(file="T19_6_gfblup_variances_all_9001_10000.rds")
+T19_6_gfblup_variances_all_10001_11000=readRDS(file="T19_6_gfblup_variances_all_10001_11000.rds")
+T19_6_gfblup_variances_all_11001_12419=readRDS(file="T19_6_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T19_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_6_gfblup_variances_all=rep(list(list()),cycles)
+T19_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_1_1000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_1001_2000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_2001_3000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_3001_4000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_4001_5000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_5001_6000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_6001_7000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_7001_8000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_8001_9000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_9001_10000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_10001_11000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_11001_12419[[r]])
+
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_1_1000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_1001_2000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_2001_3000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_3001_4000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_4001_5000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_5001_6000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_6001_7000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_7001_8000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_8001_9000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_9001_10000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_10001_11000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T19_6_gfblup_prediction_all,"T19_6_gfblup_prediction_all.rds")
+saveRDS(T19_6_gfblup_variances_all,"T19_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_7_gblup_prediction_all_1_1000=readRDS(file="T19_7_gblup_prediction_all_1_1000.rds")
+T19_7_gblup_prediction_all_1001_2000=readRDS(file="T19_7_gblup_prediction_all_1001_2000.rds")
+T19_7_gblup_prediction_all_2001_3000=readRDS(file="T19_7_gblup_prediction_all_2001_3000.rds")
+T19_7_gblup_prediction_all_3001_4000=readRDS(file="T19_7_gblup_prediction_all_3001_4000.rds")
+T19_7_gblup_prediction_all_4001_5000=readRDS(file="T19_7_gblup_prediction_all_4001_5000.rds")
+T19_7_gblup_prediction_all_5001_6000=readRDS(file="T19_7_gblup_prediction_all_5001_6000.rds")
+T19_7_gblup_prediction_all_6001_7000=readRDS(file="T19_7_gblup_prediction_all_6001_7000.rds")
+T19_7_gblup_prediction_all_7001_8000=readRDS(file="T19_7_gblup_prediction_all_7001_8000.rds")
+T19_7_gblup_prediction_all_8001_9000=readRDS(file="T19_7_gblup_prediction_all_8001_9000.rds")
+T19_7_gblup_prediction_all_9001_10000=readRDS(file="T19_7_gblup_prediction_all_9001_10000.rds")
+T19_7_gblup_prediction_all_10001_11000=readRDS(file="T19_7_gblup_prediction_all_10001_11000.rds")
+T19_7_gblup_prediction_all_11001_12419=readRDS(file="T19_7_gblup_prediction_all_11001_12419.rds")
+T19_7_gblup_prediction_all=c(T19_7_gblup_prediction_all_1_1000,T19_7_gblup_prediction_all_1001_2000,T19_7_gblup_prediction_all_2001_3000,T19_7_gblup_prediction_all_3001_4000,T19_7_gblup_prediction_all_4001_5000,T19_7_gblup_prediction_all_5001_6000,T19_7_gblup_prediction_all_6001_7000,T19_7_gblup_prediction_all_7001_8000,T19_7_gblup_prediction_all_8001_9000,T19_7_gblup_prediction_all_9001_10000,T19_7_gblup_prediction_all_10001_11000,T19_7_gblup_prediction_all_11001_12419)
+
+T19_7_gblup_variances_all_1_1000=readRDS(file="T19_7_gblup_variances_all_1_1000.rds")
+T19_7_gblup_variances_all_1001_2000=readRDS(file="T19_7_gblup_variances_all_1001_2000.rds")
+T19_7_gblup_variances_all_2001_3000=readRDS(file="T19_7_gblup_variances_all_2001_3000.rds")
+T19_7_gblup_variances_all_3001_4000=readRDS(file="T19_7_gblup_variances_all_3001_4000.rds")
+T19_7_gblup_variances_all_4001_5000=readRDS(file="T19_7_gblup_variances_all_4001_5000.rds")
+T19_7_gblup_variances_all_5001_6000=readRDS(file="T19_7_gblup_variances_all_5001_6000.rds")
+T19_7_gblup_variances_all_6001_7000=readRDS(file="T19_7_gblup_variances_all_6001_7000.rds")
+T19_7_gblup_variances_all_7001_8000=readRDS(file="T19_7_gblup_variances_all_7001_8000.rds")
+T19_7_gblup_variances_all_8001_9000=readRDS(file="T19_7_gblup_variances_all_8001_9000.rds")
+T19_7_gblup_variances_all_9001_10000=readRDS(file="T19_7_gblup_variances_all_9001_10000.rds")
+T19_7_gblup_variances_all_10001_11000=readRDS(file="T19_7_gblup_variances_all_10001_11000.rds")
+T19_7_gblup_variances_all_11001_12419=readRDS(file="T19_7_gblup_variances_all_11001_12419.rds")
+T19_7_gblup_variances_all=c(T19_7_gblup_variances_all_1_1000,T19_7_gblup_variances_all_1001_2000,T19_7_gblup_variances_all_2001_3000,T19_7_gblup_variances_all_3001_4000,T19_7_gblup_variances_all_4001_5000,T19_7_gblup_variances_all_5001_6000,T19_7_gblup_variances_all_6001_7000,T19_7_gblup_variances_all_7001_8000,T19_7_gblup_variances_all_8001_9000,T19_7_gblup_variances_all_9001_10000,T19_7_gblup_variances_all_10001_11000,T19_7_gblup_variances_all_11001_12419)
+
+saveRDS(T19_7_gblup_prediction_all,"T19_7_gblup_prediction_all.rds")
+saveRDS(T19_7_gblup_variances_all,"T19_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_7_gfblup_prediction_all_1_1000=readRDS(file="T19_7_gfblup_prediction_all_1_1000.rds")
+T19_7_gfblup_prediction_all_1001_2000=readRDS(file="T19_7_gfblup_prediction_all_1001_2000.rds")
+T19_7_gfblup_prediction_all_2001_3000=readRDS(file="T19_7_gfblup_prediction_all_2001_3000.rds")
+T19_7_gfblup_prediction_all_3001_4000=readRDS(file="T19_7_gfblup_prediction_all_3001_4000.rds")
+T19_7_gfblup_prediction_all_4001_5000=readRDS(file="T19_7_gfblup_prediction_all_4001_5000.rds")
+T19_7_gfblup_prediction_all_5001_6000=readRDS(file="T19_7_gfblup_prediction_all_5001_6000.rds")
+T19_7_gfblup_prediction_all_6001_7000=readRDS(file="T19_7_gfblup_prediction_all_6001_7000.rds")
+T19_7_gfblup_prediction_all_7001_8000=readRDS(file="T19_7_gfblup_prediction_all_7001_8000.rds")
+T19_7_gfblup_prediction_all_8001_9000=readRDS(file="T19_7_gfblup_prediction_all_8001_9000.rds")
+T19_7_gfblup_prediction_all_9001_10000=readRDS(file="T19_7_gfblup_prediction_all_9001_10000.rds")
+T19_7_gfblup_prediction_all_10001_11000=readRDS(file="T19_7_gfblup_prediction_all_10001_11000.rds")
+T19_7_gfblup_prediction_all_11001_12419=readRDS(file="T19_7_gfblup_prediction_all_11001_12419.rds")
+
+T19_7_gfblup_variances_all_1_1000=readRDS(file="T19_7_gfblup_variances_all_1_1000.rds")
+T19_7_gfblup_variances_all_1001_2000=readRDS(file="T19_7_gfblup_variances_all_1001_2000.rds")
+T19_7_gfblup_variances_all_2001_3000=readRDS(file="T19_7_gfblup_variances_all_2001_3000.rds")
+T19_7_gfblup_variances_all_3001_4000=readRDS(file="T19_7_gfblup_variances_all_3001_4000.rds")
+T19_7_gfblup_variances_all_4001_5000=readRDS(file="T19_7_gfblup_variances_all_4001_5000.rds")
+T19_7_gfblup_variances_all_5001_6000=readRDS(file="T19_7_gfblup_variances_all_5001_6000.rds")
+T19_7_gfblup_variances_all_6001_7000=readRDS(file="T19_7_gfblup_variances_all_6001_7000.rds")
+T19_7_gfblup_variances_all_7001_8000=readRDS(file="T19_7_gfblup_variances_all_7001_8000.rds")
+T19_7_gfblup_variances_all_8001_9000=readRDS(file="T19_7_gfblup_variances_all_8001_9000.rds")
+T19_7_gfblup_variances_all_9001_10000=readRDS(file="T19_7_gfblup_variances_all_9001_10000.rds")
+T19_7_gfblup_variances_all_10001_11000=readRDS(file="T19_7_gfblup_variances_all_10001_11000.rds")
+T19_7_gfblup_variances_all_11001_12419=readRDS(file="T19_7_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T19_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_7_gfblup_variances_all=rep(list(list()),cycles)
+T19_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_1_1000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_1001_2000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_2001_3000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_3001_4000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_4001_5000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_5001_6000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_6001_7000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_7001_8000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_8001_9000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_9001_10000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_10001_11000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_11001_12419[[r]])
+
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_1_1000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_1001_2000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_2001_3000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_3001_4000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_4001_5000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_5001_6000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_6001_7000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_7001_8000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_8001_9000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_9001_10000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_10001_11000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T19_7_gfblup_prediction_all,"T19_7_gfblup_prediction_all.rds")
+saveRDS(T19_7_gfblup_variances_all,"T19_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_8_gblup_prediction_all_1_1000=readRDS(file="T19_8_gblup_prediction_all_1_1000.rds")
+T19_8_gblup_prediction_all_1001_2000=readRDS(file="T19_8_gblup_prediction_all_1001_2000.rds")
+T19_8_gblup_prediction_all_2001_3000=readRDS(file="T19_8_gblup_prediction_all_2001_3000.rds")
+T19_8_gblup_prediction_all_3001_4000=readRDS(file="T19_8_gblup_prediction_all_3001_4000.rds")
+T19_8_gblup_prediction_all_4001_5000=readRDS(file="T19_8_gblup_prediction_all_4001_5000.rds")
+T19_8_gblup_prediction_all_5001_6000=readRDS(file="T19_8_gblup_prediction_all_5001_6000.rds")
+T19_8_gblup_prediction_all_6001_7000=readRDS(file="T19_8_gblup_prediction_all_6001_7000.rds")
+T19_8_gblup_prediction_all_7001_8000=readRDS(file="T19_8_gblup_prediction_all_7001_8000.rds")
+T19_8_gblup_prediction_all_8001_9000=readRDS(file="T19_8_gblup_prediction_all_8001_9000.rds")
+T19_8_gblup_prediction_all_9001_10000=readRDS(file="T19_8_gblup_prediction_all_9001_10000.rds")
+T19_8_gblup_prediction_all_10001_11000=readRDS(file="T19_8_gblup_prediction_all_10001_11000.rds")
+T19_8_gblup_prediction_all_11001_12419=readRDS(file="T19_8_gblup_prediction_all_11001_12419.rds")
+T19_8_gblup_prediction_all=c(T19_8_gblup_prediction_all_1_1000,T19_8_gblup_prediction_all_1001_2000,T19_8_gblup_prediction_all_2001_3000,T19_8_gblup_prediction_all_3001_4000,T19_8_gblup_prediction_all_4001_5000,T19_8_gblup_prediction_all_5001_6000,T19_8_gblup_prediction_all_6001_7000,T19_8_gblup_prediction_all_7001_8000,T19_8_gblup_prediction_all_8001_9000,T19_8_gblup_prediction_all_9001_10000,T19_8_gblup_prediction_all_10001_11000,T19_8_gblup_prediction_all_11001_12419)
+
+T19_8_gblup_variances_all_1_1000=readRDS(file="T19_8_gblup_variances_all_1_1000.rds")
+T19_8_gblup_variances_all_1001_2000=readRDS(file="T19_8_gblup_variances_all_1001_2000.rds")
+T19_8_gblup_variances_all_2001_3000=readRDS(file="T19_8_gblup_variances_all_2001_3000.rds")
+T19_8_gblup_variances_all_3001_4000=readRDS(file="T19_8_gblup_variances_all_3001_4000.rds")
+T19_8_gblup_variances_all_4001_5000=readRDS(file="T19_8_gblup_variances_all_4001_5000.rds")
+T19_8_gblup_variances_all_5001_6000=readRDS(file="T19_8_gblup_variances_all_5001_6000.rds")
+T19_8_gblup_variances_all_6001_7000=readRDS(file="T19_8_gblup_variances_all_6001_7000.rds")
+T19_8_gblup_variances_all_7001_8000=readRDS(file="T19_8_gblup_variances_all_7001_8000.rds")
+T19_8_gblup_variances_all_8001_9000=readRDS(file="T19_8_gblup_variances_all_8001_9000.rds")
+T19_8_gblup_variances_all_9001_10000=readRDS(file="T19_8_gblup_variances_all_9001_10000.rds")
+T19_8_gblup_variances_all_10001_11000=readRDS(file="T19_8_gblup_variances_all_10001_11000.rds")
+T19_8_gblup_variances_all_11001_12419=readRDS(file="T19_8_gblup_variances_all_11001_12419.rds")
+T19_8_gblup_variances_all=c(T19_8_gblup_variances_all_1_1000,T19_8_gblup_variances_all_1001_2000,T19_8_gblup_variances_all_2001_3000,T19_8_gblup_variances_all_3001_4000,T19_8_gblup_variances_all_4001_5000,T19_8_gblup_variances_all_5001_6000,T19_8_gblup_variances_all_6001_7000,T19_8_gblup_variances_all_7001_8000,T19_8_gblup_variances_all_8001_9000,T19_8_gblup_variances_all_9001_10000,T19_8_gblup_variances_all_10001_11000,T19_8_gblup_variances_all_11001_12419)
+
+saveRDS(T19_8_gblup_prediction_all,"T19_8_gblup_prediction_all.rds")
+saveRDS(T19_8_gblup_variances_all,"T19_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_8_gfblup_prediction_all_1_1000=readRDS(file="T19_8_gfblup_prediction_all_1_1000.rds")
+T19_8_gfblup_prediction_all_1001_2000=readRDS(file="T19_8_gfblup_prediction_all_1001_2000.rds")
+T19_8_gfblup_prediction_all_2001_3000=readRDS(file="T19_8_gfblup_prediction_all_2001_3000.rds")
+T19_8_gfblup_prediction_all_3001_4000=readRDS(file="T19_8_gfblup_prediction_all_3001_4000.rds")
+T19_8_gfblup_prediction_all_4001_5000=readRDS(file="T19_8_gfblup_prediction_all_4001_5000.rds")
+T19_8_gfblup_prediction_all_5001_6000=readRDS(file="T19_8_gfblup_prediction_all_5001_6000.rds")
+T19_8_gfblup_prediction_all_6001_7000=readRDS(file="T19_8_gfblup_prediction_all_6001_7000.rds")
+T19_8_gfblup_prediction_all_7001_8000=readRDS(file="T19_8_gfblup_prediction_all_7001_8000.rds")
+T19_8_gfblup_prediction_all_8001_9000=readRDS(file="T19_8_gfblup_prediction_all_8001_9000.rds")
+T19_8_gfblup_prediction_all_9001_10000=readRDS(file="T19_8_gfblup_prediction_all_9001_10000.rds")
+T19_8_gfblup_prediction_all_10001_11000=readRDS(file="T19_8_gfblup_prediction_all_10001_11000.rds")
+T19_8_gfblup_prediction_all_11001_12419=readRDS(file="T19_8_gfblup_prediction_all_11001_12419.rds")
+
+T19_8_gfblup_variances_all_1_1000=readRDS(file="T19_8_gfblup_variances_all_1_1000.rds")
+T19_8_gfblup_variances_all_1001_2000=readRDS(file="T19_8_gfblup_variances_all_1001_2000.rds")
+T19_8_gfblup_variances_all_2001_3000=readRDS(file="T19_8_gfblup_variances_all_2001_3000.rds")
+T19_8_gfblup_variances_all_3001_4000=readRDS(file="T19_8_gfblup_variances_all_3001_4000.rds")
+T19_8_gfblup_variances_all_4001_5000=readRDS(file="T19_8_gfblup_variances_all_4001_5000.rds")
+T19_8_gfblup_variances_all_5001_6000=readRDS(file="T19_8_gfblup_variances_all_5001_6000.rds")
+T19_8_gfblup_variances_all_6001_7000=readRDS(file="T19_8_gfblup_variances_all_6001_7000.rds")
+T19_8_gfblup_variances_all_7001_8000=readRDS(file="T19_8_gfblup_variances_all_7001_8000.rds")
+T19_8_gfblup_variances_all_8001_9000=readRDS(file="T19_8_gfblup_variances_all_8001_9000.rds")
+T19_8_gfblup_variances_all_9001_10000=readRDS(file="T19_8_gfblup_variances_all_9001_10000.rds")
+T19_8_gfblup_variances_all_10001_11000=readRDS(file="T19_8_gfblup_variances_all_10001_11000.rds")
+T19_8_gfblup_variances_all_11001_12419=readRDS(file="T19_8_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T19_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_8_gfblup_variances_all=rep(list(list()),cycles)
+T19_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_1_1000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_1001_2000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_2001_3000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_3001_4000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_4001_5000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_5001_6000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_6001_7000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_7001_8000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_8001_9000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_9001_10000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_10001_11000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_11001_12419[[r]])
+
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_1_1000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_1001_2000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_2001_3000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_3001_4000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_4001_5000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_5001_6000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_6001_7000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_7001_8000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_8001_9000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_9001_10000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_10001_11000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T19_8_gfblup_prediction_all,"T19_8_gfblup_prediction_all.rds")
+saveRDS(T19_8_gfblup_variances_all,"T19_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T20_1_gblup_prediction_all_1_1000=readRDS(file="T20_1_gblup_prediction_all_1_1000.rds")
+T20_1_gblup_prediction_all_1001_2000=readRDS(file="T20_1_gblup_prediction_all_1001_2000.rds")
+T20_1_gblup_prediction_all_2001_3000=readRDS(file="T20_1_gblup_prediction_all_2001_3000.rds")
+T20_1_gblup_prediction_all_3001_4000=readRDS(file="T20_1_gblup_prediction_all_3001_4000.rds")
+T20_1_gblup_prediction_all_4001_5000=readRDS(file="T20_1_gblup_prediction_all_4001_5000.rds")
+T20_1_gblup_prediction_all_5001_6000=readRDS(file="T20_1_gblup_prediction_all_5001_6000.rds")
+T20_1_gblup_prediction_all_6001_7000=readRDS(file="T20_1_gblup_prediction_all_6001_7000.rds")
+T20_1_gblup_prediction_all_7001_8000=readRDS(file="T20_1_gblup_prediction_all_7001_8000.rds")
+T20_1_gblup_prediction_all_8001_9000=readRDS(file="T20_1_gblup_prediction_all_8001_9000.rds")
+T20_1_gblup_prediction_all_9001_10000=readRDS(file="T20_1_gblup_prediction_all_9001_10000.rds")
+T20_1_gblup_prediction_all_10001_11000=readRDS(file="T20_1_gblup_prediction_all_10001_11000.rds")
+T20_1_gblup_prediction_all_11001_12419=readRDS(file="T20_1_gblup_prediction_all_11001_12419.rds")
+T20_1_gblup_prediction_all=c(T20_1_gblup_prediction_all_1_1000,T20_1_gblup_prediction_all_1001_2000,T20_1_gblup_prediction_all_2001_3000,T20_1_gblup_prediction_all_3001_4000,T20_1_gblup_prediction_all_4001_5000,T20_1_gblup_prediction_all_5001_6000,T20_1_gblup_prediction_all_6001_7000,T20_1_gblup_prediction_all_7001_8000,T20_1_gblup_prediction_all_8001_9000,T20_1_gblup_prediction_all_9001_10000,T20_1_gblup_prediction_all_10001_11000,T20_1_gblup_prediction_all_11001_12419)
+
+T20_1_gblup_variances_all_1_1000=readRDS(file="T20_1_gblup_variances_all_1_1000.rds")
+T20_1_gblup_variances_all_1001_2000=readRDS(file="T20_1_gblup_variances_all_1001_2000.rds")
+T20_1_gblup_variances_all_2001_3000=readRDS(file="T20_1_gblup_variances_all_2001_3000.rds")
+T20_1_gblup_variances_all_3001_4000=readRDS(file="T20_1_gblup_variances_all_3001_4000.rds")
+T20_1_gblup_variances_all_4001_5000=readRDS(file="T20_1_gblup_variances_all_4001_5000.rds")
+T20_1_gblup_variances_all_5001_6000=readRDS(file="T20_1_gblup_variances_all_5001_6000.rds")
+T20_1_gblup_variances_all_6001_7000=readRDS(file="T20_1_gblup_variances_all_6001_7000.rds")
+T20_1_gblup_variances_all_7001_8000=readRDS(file="T20_1_gblup_variances_all_7001_8000.rds")
+T20_1_gblup_variances_all_8001_9000=readRDS(file="T20_1_gblup_variances_all_8001_9000.rds")
+T20_1_gblup_variances_all_9001_10000=readRDS(file="T20_1_gblup_variances_all_9001_10000.rds")
+T20_1_gblup_variances_all_10001_11000=readRDS(file="T20_1_gblup_variances_all_10001_11000.rds")
+T20_1_gblup_variances_all_11001_12419=readRDS(file="T20_1_gblup_variances_all_11001_12419.rds")
+T20_1_gblup_variances_all=c(T20_1_gblup_variances_all_1_1000,T20_1_gblup_variances_all_1001_2000,T20_1_gblup_variances_all_2001_3000,T20_1_gblup_variances_all_3001_4000,T20_1_gblup_variances_all_4001_5000,T20_1_gblup_variances_all_5001_6000,T20_1_gblup_variances_all_6001_7000,T20_1_gblup_variances_all_7001_8000,T20_1_gblup_variances_all_8001_9000,T20_1_gblup_variances_all_9001_10000,T20_1_gblup_variances_all_10001_11000,T20_1_gblup_variances_all_11001_12419)
+
+saveRDS(T20_1_gblup_prediction_all,"T20_1_gblup_prediction_all.rds")
+saveRDS(T20_1_gblup_variances_all,"T20_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T20_1_gfblup_prediction_all_1_1000=readRDS(file="T20_1_gfblup_prediction_all_1_1000.rds")
+T20_1_gfblup_prediction_all_1001_2000=readRDS(file="T20_1_gfblup_prediction_all_1001_2000.rds")
+T20_1_gfblup_prediction_all_2001_3000=readRDS(file="T20_1_gfblup_prediction_all_2001_3000.rds")
+T20_1_gfblup_prediction_all_3001_4000=readRDS(file="T20_1_gfblup_prediction_all_3001_4000.rds")
+T20_1_gfblup_prediction_all_4001_5000=readRDS(file="T20_1_gfblup_prediction_all_4001_5000.rds")
+T20_1_gfblup_prediction_all_5001_6000=readRDS(file="T20_1_gfblup_prediction_all_5001_6000.rds")
+T20_1_gfblup_prediction_all_6001_7000=readRDS(file="T20_1_gfblup_prediction_all_6001_7000.rds")
+T20_1_gfblup_prediction_all_7001_8000=readRDS(file="T20_1_gfblup_prediction_all_7001_8000.rds")
+T20_1_gfblup_prediction_all_8001_9000=readRDS(file="T20_1_gfblup_prediction_all_8001_9000.rds")
+T20_1_gfblup_prediction_all_9001_10000=readRDS(file="T20_1_gfblup_prediction_all_9001_10000.rds")
+T20_1_gfblup_prediction_all_10001_11000=readRDS(file="T20_1_gfblup_prediction_all_10001_11000.rds")
+T20_1_gfblup_prediction_all_11001_12419=readRDS(file="T20_1_gfblup_prediction_all_11001_12419.rds")
+
+T20_1_gfblup_variances_all_1_1000=readRDS(file="T20_1_gfblup_variances_all_1_1000.rds")
+T20_1_gfblup_variances_all_1001_2000=readRDS(file="T20_1_gfblup_variances_all_1001_2000.rds")
+T20_1_gfblup_variances_all_2001_3000=readRDS(file="T20_1_gfblup_variances_all_2001_3000.rds")
+T20_1_gfblup_variances_all_3001_4000=readRDS(file="T20_1_gfblup_variances_all_3001_4000.rds")
+T20_1_gfblup_variances_all_4001_5000=readRDS(file="T20_1_gfblup_variances_all_4001_5000.rds")
+T20_1_gfblup_variances_all_5001_6000=readRDS(file="T20_1_gfblup_variances_all_5001_6000.rds")
+T20_1_gfblup_variances_all_6001_7000=readRDS(file="T20_1_gfblup_variances_all_6001_7000.rds")
+T20_1_gfblup_variances_all_7001_8000=readRDS(file="T20_1_gfblup_variances_all_7001_8000.rds")
+T20_1_gfblup_variances_all_8001_9000=readRDS(file="T20_1_gfblup_variances_all_8001_9000.rds")
+T20_1_gfblup_variances_all_9001_10000=readRDS(file="T20_1_gfblup_variances_all_9001_10000.rds")
+T20_1_gfblup_variances_all_10001_11000=readRDS(file="T20_1_gfblup_variances_all_10001_11000.rds")
+T20_1_gfblup_variances_all_11001_12419=readRDS(file="T20_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T20_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T20_1_gfblup_variances_all=rep(list(list()),cycles)
+T20_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_1_1000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_1001_2000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_2001_3000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_3001_4000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_4001_5000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_5001_6000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_6001_7000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_7001_8000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_8001_9000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_9001_10000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_10001_11000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_11001_12419[[r]])
+
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_1_1000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_1001_2000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_2001_3000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_3001_4000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_4001_5000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_5001_6000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_6001_7000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_7001_8000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_8001_9000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_9001_10000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_10001_11000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T20_1_gfblup_prediction_all,"T20_1_gfblup_prediction_all.rds")
+saveRDS(T20_1_gfblup_variances_all,"T20_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T20_2_gblup_prediction_all_1_1000=readRDS(file="T20_2_gblup_prediction_all_1_1000.rds")
+T20_2_gblup_prediction_all_1001_2000=readRDS(file="T20_2_gblup_prediction_all_1001_2000.rds")
+T20_2_gblup_prediction_all_2001_3000=readRDS(file="T20_2_gblup_prediction_all_2001_3000.rds")
+T20_2_gblup_prediction_all_3001_4000=readRDS(file="T20_2_gblup_prediction_all_3001_4000.rds")
+T20_2_gblup_prediction_all_4001_5000=readRDS(file="T20_2_gblup_prediction_all_4001_5000.rds")
+T20_2_gblup_prediction_all_5001_6000=readRDS(file="T20_2_gblup_prediction_all_5001_6000.rds")
+T20_2_gblup_prediction_all_6001_7000=readRDS(file="T20_2_gblup_prediction_all_6001_7000.rds")
+T20_2_gblup_prediction_all_7001_8000=readRDS(file="T20_2_gblup_prediction_all_7001_8000.rds")
+T20_2_gblup_prediction_all_8001_9000=readRDS(file="T20_2_gblup_prediction_all_8001_9000.rds")
+T20_2_gblup_prediction_all_9001_10000=readRDS(file="T20_2_gblup_prediction_all_9001_10000.rds")
+T20_2_gblup_prediction_all_10001_11000=readRDS(file="T20_2_gblup_prediction_all_10001_11000.rds")
+T20_2_gblup_prediction_all_11001_12419=readRDS(file="T20_2_gblup_prediction_all_11001_12419.rds")
+T20_2_gblup_prediction_all=c(T20_2_gblup_prediction_all_1_1000,T20_2_gblup_prediction_all_1001_2000,T20_2_gblup_prediction_all_2001_3000,T20_2_gblup_prediction_all_3001_4000,T20_2_gblup_prediction_all_4001_5000,T20_2_gblup_prediction_all_5001_6000,T20_2_gblup_prediction_all_6001_7000,T20_2_gblup_prediction_all_7001_8000,T20_2_gblup_prediction_all_8001_9000,T20_2_gblup_prediction_all_9001_10000,T20_2_gblup_prediction_all_10001_11000,T20_2_gblup_prediction_all_11001_12419)
+
+T20_2_gblup_variances_all_1_1000=readRDS(file="T20_2_gblup_variances_all_1_1000.rds")
+T20_2_gblup_variances_all_1001_2000=readRDS(file="T20_2_gblup_variances_all_1001_2000.rds")
+T20_2_gblup_variances_all_2001_3000=readRDS(file="T20_2_gblup_variances_all_2001_3000.rds")
+T20_2_gblup_variances_all_3001_4000=readRDS(file="T20_2_gblup_variances_all_3001_4000.rds")
+T20_2_gblup_variances_all_4001_5000=readRDS(file="T20_2_gblup_variances_all_4001_5000.rds")
+T20_2_gblup_variances_all_5001_6000=readRDS(file="T20_2_gblup_variances_all_5001_6000.rds")
+T20_2_gblup_variances_all_6001_7000=readRDS(file="T20_2_gblup_variances_all_6001_7000.rds")
+T20_2_gblup_variances_all_7001_8000=readRDS(file="T20_2_gblup_variances_all_7001_8000.rds")
+T20_2_gblup_variances_all_8001_9000=readRDS(file="T20_2_gblup_variances_all_8001_9000.rds")
+T20_2_gblup_variances_all_9001_10000=readRDS(file="T20_2_gblup_variances_all_9001_10000.rds")
+T20_2_gblup_variances_all_10001_11000=readRDS(file="T20_2_gblup_variances_all_10001_11000.rds")
+T20_2_gblup_variances_all_11001_12419=readRDS(file="T20_2_gblup_variances_all_11001_12419.rds")
+T20_2_gblup_variances_all=c(T20_2_gblup_variances_all_1_1000,T20_2_gblup_variances_all_1001_2000,T20_2_gblup_variances_all_2001_3000,T20_2_gblup_variances_all_3001_4000,T20_2_gblup_variances_all_4001_5000,T20_2_gblup_variances_all_5001_6000,T20_2_gblup_variances_all_6001_7000,T20_2_gblup_variances_all_7001_8000,T20_2_gblup_variances_all_8001_9000,T20_2_gblup_variances_all_9001_10000,T20_2_gblup_variances_all_10001_11000,T20_2_gblup_variances_all_11001_12419)
+
+saveRDS(T20_2_gblup_prediction_all,"T20_2_gblup_prediction_all.rds")
+saveRDS(T20_2_gblup_variances_all,"T20_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T20_2_gfblup_prediction_all_1_1000=readRDS(file="T20_2_gfblup_prediction_all_1_1000.rds")
+T20_2_gfblup_prediction_all_1001_2000=readRDS(file="T20_2_gfblup_prediction_all_1001_2000.rds")
+T20_2_gfblup_prediction_all_2001_3000=readRDS(file="T20_2_gfblup_prediction_all_2001_3000.rds")
+T20_2_gfblup_prediction_all_3001_4000=readRDS(file="T20_2_gfblup_prediction_all_3001_4000.rds")
+T20_2_gfblup_prediction_all_4001_5000=readRDS(file="T20_2_gfblup_prediction_all_4001_5000.rds")
+T20_2_gfblup_prediction_all_5001_6000=readRDS(file="T20_2_gfblup_prediction_all_5001_6000.rds")
+T20_2_gfblup_prediction_all_6001_7000=readRDS(file="T20_2_gfblup_prediction_all_6001_7000.rds")
+T20_2_gfblup_prediction_all_7001_8000=readRDS(file="T20_2_gfblup_prediction_all_7001_8000.rds")
+T20_2_gfblup_prediction_all_8001_9000=readRDS(file="T20_2_gfblup_prediction_all_8001_9000.rds")
+T20_2_gfblup_prediction_all_9001_10000=readRDS(file="T20_2_gfblup_prediction_all_9001_10000.rds")
+T20_2_gfblup_prediction_all_10001_11000=readRDS(file="T20_2_gfblup_prediction_all_10001_11000.rds")
+T20_2_gfblup_prediction_all_11001_12419=readRDS(file="T20_2_gfblup_prediction_all_11001_12419.rds")
+
+T20_2_gfblup_variances_all_1_1000=readRDS(file="T20_2_gfblup_variances_all_1_1000.rds")
+T20_2_gfblup_variances_all_1001_2000=readRDS(file="T20_2_gfblup_variances_all_1001_2000.rds")
+T20_2_gfblup_variances_all_2001_3000=readRDS(file="T20_2_gfblup_variances_all_2001_3000.rds")
+T20_2_gfblup_variances_all_3001_4000=readRDS(file="T20_2_gfblup_variances_all_3001_4000.rds")
+T20_2_gfblup_variances_all_4001_5000=readRDS(file="T20_2_gfblup_variances_all_4001_5000.rds")
+T20_2_gfblup_variances_all_5001_6000=readRDS(file="T20_2_gfblup_variances_all_5001_6000.rds")
+T20_2_gfblup_variances_all_6001_7000=readRDS(file="T20_2_gfblup_variances_all_6001_7000.rds")
+T20_2_gfblup_variances_all_7001_8000=readRDS(file="T20_2_gfblup_variances_all_7001_8000.rds")
+T20_2_gfblup_variances_all_8001_9000=readRDS(file="T20_2_gfblup_variances_all_8001_9000.rds")
+T20_2_gfblup_variances_all_9001_10000=readRDS(file="T20_2_gfblup_variances_all_9001_10000.rds")
+T20_2_gfblup_variances_all_10001_11000=readRDS(file="T20_2_gfblup_variances_all_10001_11000.rds")
+T20_2_gfblup_variances_all_11001_12419=readRDS(file="T20_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(T20_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T20_2_gfblup_variances_all=rep(list(list()),cycles)
+T20_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_1_1000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_1001_2000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_2001_3000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_3001_4000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_4001_5000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_5001_6000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_6001_7000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_7001_8000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_8001_9000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_9001_10000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_10001_11000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_11001_12419[[r]])
+
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_1_1000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_1001_2000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_2001_3000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_3001_4000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_4001_5000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_5001_6000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_6001_7000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_7001_8000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_8001_9000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_9001_10000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_10001_11000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(T20_2_gfblup_prediction_all,"T20_2_gfblup_prediction_all.rds")
+saveRDS(T20_2_gfblup_variances_all,"T20_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
diff --git a/code/using_COEX/pla/gblup_vs_gfblup_using_coexpression_analysis1.R b/code/using_COEX/pla/gblup_vs_gfblup_using_coexpression_analysis1.R
index 2e82e61..816f0dc 100644
--- a/code/using_COEX/pla/gblup_vs_gfblup_using_coexpression_analysis1.R
+++ b/code/using_COEX/pla/gblup_vs_gfblup_using_coexpression_analysis1.R
@@ -2,11 +2,27 @@
 ##################################################################################################################################
 #	A	N	A	L	Y	S	I	S
 ##################################################################################################################################
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_COEX/pla/8fold/")
-
-all_coexpression_clusters <-as.data.frame(read.table(file ="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE))
-coex_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers_number.rds")
-coex_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers.rds")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+setwd(paste0(wdir,"/",wd,"/8fold/"));
+##################################################################################################################################
+all_coexpression_clusters <-as.data.frame(read.table(file ="../data/priors/coexpression/ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE))
+coex_markers_number=readRDS(file="../data/priors/coexpression/coex_markers_number.rds")
+coex_markers=readRDS(file="../data/priors/coexpression/coex_markers.rds")
 ###################################################################################################################################
 T20_2_gblup_variances_all=readRDS(file="./T20_2_gblup_variances_all.rds")
 T20_2_gblup_prediction_all=readRDS(file="./T20_2_gblup_prediction_all.rds")
diff --git a/code/using_COEX/psii/8fold/combine.R b/code/using_COEX/psii/8fold/combine.R
new file mode 100644
index 0000000..cbc91f9
--- /dev/null
+++ b/code/using_COEX/psii/8fold/combine.R
@@ -0,0 +1,1766 @@
+##################################################################################################################################
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+setwd(paste0(wdir,"/",wd));
+##################################################################################################################################
+
+L1_1_gblup_prediction_all_1_1000=readRDS(file="L1_1_gblup_prediction_all_1_1000.rds")
+L1_1_gblup_prediction_all_1001_2000=readRDS(file="L1_1_gblup_prediction_all_1001_2000.rds")
+L1_1_gblup_prediction_all_2001_3000=readRDS(file="L1_1_gblup_prediction_all_2001_3000.rds")
+L1_1_gblup_prediction_all_3001_4000=readRDS(file="L1_1_gblup_prediction_all_3001_4000.rds")
+L1_1_gblup_prediction_all_4001_5000=readRDS(file="L1_1_gblup_prediction_all_4001_5000.rds")
+L1_1_gblup_prediction_all_5001_6000=readRDS(file="L1_1_gblup_prediction_all_5001_6000.rds")
+L1_1_gblup_prediction_all_6001_7000=readRDS(file="L1_1_gblup_prediction_all_6001_7000.rds")
+L1_1_gblup_prediction_all_7001_8000=readRDS(file="L1_1_gblup_prediction_all_7001_8000.rds")
+L1_1_gblup_prediction_all_8001_9000=readRDS(file="L1_1_gblup_prediction_all_8001_9000.rds")
+L1_1_gblup_prediction_all_9001_10000=readRDS(file="L1_1_gblup_prediction_all_9001_10000.rds")
+L1_1_gblup_prediction_all_10001_11000=readRDS(file="L1_1_gblup_prediction_all_10001_11000.rds")
+L1_1_gblup_prediction_all_11001_12419=readRDS(file="L1_1_gblup_prediction_all_11001_12419.rds")
+L1_1_gblup_prediction_all=c(L1_1_gblup_prediction_all_1_1000,L1_1_gblup_prediction_all_1001_2000,L1_1_gblup_prediction_all_2001_3000,L1_1_gblup_prediction_all_3001_4000,L1_1_gblup_prediction_all_4001_5000,L1_1_gblup_prediction_all_5001_6000,L1_1_gblup_prediction_all_6001_7000,L1_1_gblup_prediction_all_7001_8000,L1_1_gblup_prediction_all_8001_9000,L1_1_gblup_prediction_all_9001_10000,L1_1_gblup_prediction_all_10001_11000,L1_1_gblup_prediction_all_11001_12419)
+
+L1_1_gblup_variances_all_1_1000=readRDS(file="L1_1_gblup_variances_all_1_1000.rds")
+L1_1_gblup_variances_all_1001_2000=readRDS(file="L1_1_gblup_variances_all_1001_2000.rds")
+L1_1_gblup_variances_all_2001_3000=readRDS(file="L1_1_gblup_variances_all_2001_3000.rds")
+L1_1_gblup_variances_all_3001_4000=readRDS(file="L1_1_gblup_variances_all_3001_4000.rds")
+L1_1_gblup_variances_all_4001_5000=readRDS(file="L1_1_gblup_variances_all_4001_5000.rds")
+L1_1_gblup_variances_all_5001_6000=readRDS(file="L1_1_gblup_variances_all_5001_6000.rds")
+L1_1_gblup_variances_all_6001_7000=readRDS(file="L1_1_gblup_variances_all_6001_7000.rds")
+L1_1_gblup_variances_all_7001_8000=readRDS(file="L1_1_gblup_variances_all_7001_8000.rds")
+L1_1_gblup_variances_all_8001_9000=readRDS(file="L1_1_gblup_variances_all_8001_9000.rds")
+L1_1_gblup_variances_all_9001_10000=readRDS(file="L1_1_gblup_variances_all_9001_10000.rds")
+L1_1_gblup_variances_all_10001_11000=readRDS(file="L1_1_gblup_variances_all_10001_11000.rds")
+L1_1_gblup_variances_all_11001_12419=readRDS(file="L1_1_gblup_variances_all_11001_12419.rds")
+L1_1_gblup_variances_all=c(L1_1_gblup_variances_all_1_1000,L1_1_gblup_variances_all_1001_2000,L1_1_gblup_variances_all_2001_3000,L1_1_gblup_variances_all_3001_4000,L1_1_gblup_variances_all_4001_5000,L1_1_gblup_variances_all_5001_6000,L1_1_gblup_variances_all_6001_7000,L1_1_gblup_variances_all_7001_8000,L1_1_gblup_variances_all_8001_9000,L1_1_gblup_variances_all_9001_10000,L1_1_gblup_variances_all_10001_11000,L1_1_gblup_variances_all_11001_12419)
+
+saveRDS(L1_1_gblup_prediction_all,"L1_1_gblup_prediction_all.rds")
+saveRDS(L1_1_gblup_variances_all,"L1_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L1_1_gfblup_prediction_all_1_1000=readRDS(file="L1_1_gfblup_prediction_all_1_1000.rds")
+L1_1_gfblup_prediction_all_1001_2000=readRDS(file="L1_1_gfblup_prediction_all_1001_2000.rds")
+L1_1_gfblup_prediction_all_2001_3000=readRDS(file="L1_1_gfblup_prediction_all_2001_3000.rds")
+L1_1_gfblup_prediction_all_3001_4000=readRDS(file="L1_1_gfblup_prediction_all_3001_4000.rds")
+L1_1_gfblup_prediction_all_4001_5000=readRDS(file="L1_1_gfblup_prediction_all_4001_5000.rds")
+L1_1_gfblup_prediction_all_5001_6000=readRDS(file="L1_1_gfblup_prediction_all_5001_6000.rds")
+L1_1_gfblup_prediction_all_6001_7000=readRDS(file="L1_1_gfblup_prediction_all_6001_7000.rds")
+L1_1_gfblup_prediction_all_7001_8000=readRDS(file="L1_1_gfblup_prediction_all_7001_8000.rds")
+L1_1_gfblup_prediction_all_8001_9000=readRDS(file="L1_1_gfblup_prediction_all_8001_9000.rds")
+L1_1_gfblup_prediction_all_9001_10000=readRDS(file="L1_1_gfblup_prediction_all_9001_10000.rds")
+L1_1_gfblup_prediction_all_10001_11000=readRDS(file="L1_1_gfblup_prediction_all_10001_11000.rds")
+L1_1_gfblup_prediction_all_11001_12419=readRDS(file="L1_1_gfblup_prediction_all_11001_12419.rds")
+
+L1_1_gfblup_variances_all_1_1000=readRDS(file="L1_1_gfblup_variances_all_1_1000.rds")
+L1_1_gfblup_variances_all_1001_2000=readRDS(file="L1_1_gfblup_variances_all_1001_2000.rds")
+L1_1_gfblup_variances_all_2001_3000=readRDS(file="L1_1_gfblup_variances_all_2001_3000.rds")
+L1_1_gfblup_variances_all_3001_4000=readRDS(file="L1_1_gfblup_variances_all_3001_4000.rds")
+L1_1_gfblup_variances_all_4001_5000=readRDS(file="L1_1_gfblup_variances_all_4001_5000.rds")
+L1_1_gfblup_variances_all_5001_6000=readRDS(file="L1_1_gfblup_variances_all_5001_6000.rds")
+L1_1_gfblup_variances_all_6001_7000=readRDS(file="L1_1_gfblup_variances_all_6001_7000.rds")
+L1_1_gfblup_variances_all_7001_8000=readRDS(file="L1_1_gfblup_variances_all_7001_8000.rds")
+L1_1_gfblup_variances_all_8001_9000=readRDS(file="L1_1_gfblup_variances_all_8001_9000.rds")
+L1_1_gfblup_variances_all_9001_10000=readRDS(file="L1_1_gfblup_variances_all_9001_10000.rds")
+L1_1_gfblup_variances_all_10001_11000=readRDS(file="L1_1_gfblup_variances_all_10001_11000.rds")
+L1_1_gfblup_variances_all_11001_12419=readRDS(file="L1_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(L1_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L1_1_gfblup_variances_all=rep(list(list()),cycles)
+L1_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_1_1000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_1001_2000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_2001_3000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_3001_4000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_4001_5000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_5001_6000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_6001_7000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_7001_8000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_8001_9000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_9001_10000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_10001_11000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_11001_12419[[r]])
+
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_1_1000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_1001_2000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_2001_3000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_3001_4000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_4001_5000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_5001_6000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_6001_7000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_7001_8000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_8001_9000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_9001_10000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_10001_11000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(L1_1_gfblup_prediction_all,"L1_1_gfblup_prediction_all.rds")
+saveRDS(L1_1_gfblup_variances_all,"L1_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L1_2_gblup_prediction_all_1_1000=readRDS(file="L1_2_gblup_prediction_all_1_1000.rds")
+L1_2_gblup_prediction_all_1001_2000=readRDS(file="L1_2_gblup_prediction_all_1001_2000.rds")
+L1_2_gblup_prediction_all_2001_3000=readRDS(file="L1_2_gblup_prediction_all_2001_3000.rds")
+L1_2_gblup_prediction_all_3001_4000=readRDS(file="L1_2_gblup_prediction_all_3001_4000.rds")
+L1_2_gblup_prediction_all_4001_5000=readRDS(file="L1_2_gblup_prediction_all_4001_5000.rds")
+L1_2_gblup_prediction_all_5001_6000=readRDS(file="L1_2_gblup_prediction_all_5001_6000.rds")
+L1_2_gblup_prediction_all_6001_7000=readRDS(file="L1_2_gblup_prediction_all_6001_7000.rds")
+L1_2_gblup_prediction_all_7001_8000=readRDS(file="L1_2_gblup_prediction_all_7001_8000.rds")
+L1_2_gblup_prediction_all_8001_9000=readRDS(file="L1_2_gblup_prediction_all_8001_9000.rds")
+L1_2_gblup_prediction_all_9001_10000=readRDS(file="L1_2_gblup_prediction_all_9001_10000.rds")
+L1_2_gblup_prediction_all_10001_11000=readRDS(file="L1_2_gblup_prediction_all_10001_11000.rds")
+L1_2_gblup_prediction_all_11001_12419=readRDS(file="L1_2_gblup_prediction_all_11001_12419.rds")
+L1_2_gblup_prediction_all=c(L1_2_gblup_prediction_all_1_1000,L1_2_gblup_prediction_all_1001_2000,L1_2_gblup_prediction_all_2001_3000,L1_2_gblup_prediction_all_3001_4000,L1_2_gblup_prediction_all_4001_5000,L1_2_gblup_prediction_all_5001_6000,L1_2_gblup_prediction_all_6001_7000,L1_2_gblup_prediction_all_7001_8000,L1_2_gblup_prediction_all_8001_9000,L1_2_gblup_prediction_all_9001_10000,L1_2_gblup_prediction_all_10001_11000,L1_2_gblup_prediction_all_11001_12419)
+
+L1_2_gblup_variances_all_1_1000=readRDS(file="L1_2_gblup_variances_all_1_1000.rds")
+L1_2_gblup_variances_all_1001_2000=readRDS(file="L1_2_gblup_variances_all_1001_2000.rds")
+L1_2_gblup_variances_all_2001_3000=readRDS(file="L1_2_gblup_variances_all_2001_3000.rds")
+L1_2_gblup_variances_all_3001_4000=readRDS(file="L1_2_gblup_variances_all_3001_4000.rds")
+L1_2_gblup_variances_all_4001_5000=readRDS(file="L1_2_gblup_variances_all_4001_5000.rds")
+L1_2_gblup_variances_all_5001_6000=readRDS(file="L1_2_gblup_variances_all_5001_6000.rds")
+L1_2_gblup_variances_all_6001_7000=readRDS(file="L1_2_gblup_variances_all_6001_7000.rds")
+L1_2_gblup_variances_all_7001_8000=readRDS(file="L1_2_gblup_variances_all_7001_8000.rds")
+L1_2_gblup_variances_all_8001_9000=readRDS(file="L1_2_gblup_variances_all_8001_9000.rds")
+L1_2_gblup_variances_all_9001_10000=readRDS(file="L1_2_gblup_variances_all_9001_10000.rds")
+L1_2_gblup_variances_all_10001_11000=readRDS(file="L1_2_gblup_variances_all_10001_11000.rds")
+L1_2_gblup_variances_all_11001_12419=readRDS(file="L1_2_gblup_variances_all_11001_12419.rds")
+L1_2_gblup_variances_all=c(L1_2_gblup_variances_all_1_1000,L1_2_gblup_variances_all_1001_2000,L1_2_gblup_variances_all_2001_3000,L1_2_gblup_variances_all_3001_4000,L1_2_gblup_variances_all_4001_5000,L1_2_gblup_variances_all_5001_6000,L1_2_gblup_variances_all_6001_7000,L1_2_gblup_variances_all_7001_8000,L1_2_gblup_variances_all_8001_9000,L1_2_gblup_variances_all_9001_10000,L1_2_gblup_variances_all_10001_11000,L1_2_gblup_variances_all_11001_12419)
+
+saveRDS(L1_2_gblup_prediction_all,"L1_2_gblup_prediction_all.rds")
+saveRDS(L1_2_gblup_variances_all,"L1_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L1_2_gfblup_prediction_all_1_1000=readRDS(file="L1_2_gfblup_prediction_all_1_1000.rds")
+L1_2_gfblup_prediction_all_1001_2000=readRDS(file="L1_2_gfblup_prediction_all_1001_2000.rds")
+L1_2_gfblup_prediction_all_2001_3000=readRDS(file="L1_2_gfblup_prediction_all_2001_3000.rds")
+L1_2_gfblup_prediction_all_3001_4000=readRDS(file="L1_2_gfblup_prediction_all_3001_4000.rds")
+L1_2_gfblup_prediction_all_4001_5000=readRDS(file="L1_2_gfblup_prediction_all_4001_5000.rds")
+L1_2_gfblup_prediction_all_5001_6000=readRDS(file="L1_2_gfblup_prediction_all_5001_6000.rds")
+L1_2_gfblup_prediction_all_6001_7000=readRDS(file="L1_2_gfblup_prediction_all_6001_7000.rds")
+L1_2_gfblup_prediction_all_7001_8000=readRDS(file="L1_2_gfblup_prediction_all_7001_8000.rds")
+L1_2_gfblup_prediction_all_8001_9000=readRDS(file="L1_2_gfblup_prediction_all_8001_9000.rds")
+L1_2_gfblup_prediction_all_9001_10000=readRDS(file="L1_2_gfblup_prediction_all_9001_10000.rds")
+L1_2_gfblup_prediction_all_10001_11000=readRDS(file="L1_2_gfblup_prediction_all_10001_11000.rds")
+L1_2_gfblup_prediction_all_11001_12419=readRDS(file="L1_2_gfblup_prediction_all_11001_12419.rds")
+
+L1_2_gfblup_variances_all_1_1000=readRDS(file="L1_2_gfblup_variances_all_1_1000.rds")
+L1_2_gfblup_variances_all_1001_2000=readRDS(file="L1_2_gfblup_variances_all_1001_2000.rds")
+L1_2_gfblup_variances_all_2001_3000=readRDS(file="L1_2_gfblup_variances_all_2001_3000.rds")
+L1_2_gfblup_variances_all_3001_4000=readRDS(file="L1_2_gfblup_variances_all_3001_4000.rds")
+L1_2_gfblup_variances_all_4001_5000=readRDS(file="L1_2_gfblup_variances_all_4001_5000.rds")
+L1_2_gfblup_variances_all_5001_6000=readRDS(file="L1_2_gfblup_variances_all_5001_6000.rds")
+L1_2_gfblup_variances_all_6001_7000=readRDS(file="L1_2_gfblup_variances_all_6001_7000.rds")
+L1_2_gfblup_variances_all_7001_8000=readRDS(file="L1_2_gfblup_variances_all_7001_8000.rds")
+L1_2_gfblup_variances_all_8001_9000=readRDS(file="L1_2_gfblup_variances_all_8001_9000.rds")
+L1_2_gfblup_variances_all_9001_10000=readRDS(file="L1_2_gfblup_variances_all_9001_10000.rds")
+L1_2_gfblup_variances_all_10001_11000=readRDS(file="L1_2_gfblup_variances_all_10001_11000.rds")
+L1_2_gfblup_variances_all_11001_12419=readRDS(file="L1_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(L1_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L1_2_gfblup_variances_all=rep(list(list()),cycles)
+L1_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_1_1000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_1001_2000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_2001_3000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_3001_4000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_4001_5000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_5001_6000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_6001_7000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_7001_8000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_8001_9000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_9001_10000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_10001_11000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_11001_12419[[r]])
+
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_1_1000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_1001_2000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_2001_3000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_3001_4000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_4001_5000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_5001_6000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_6001_7000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_7001_8000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_8001_9000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_9001_10000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_10001_11000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(L1_2_gfblup_prediction_all,"L1_2_gfblup_prediction_all.rds")
+saveRDS(L1_2_gfblup_variances_all,"L1_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L1_3_gblup_prediction_all_1_1000=readRDS(file="L1_3_gblup_prediction_all_1_1000.rds")
+L1_3_gblup_prediction_all_1001_2000=readRDS(file="L1_3_gblup_prediction_all_1001_2000.rds")
+L1_3_gblup_prediction_all_2001_3000=readRDS(file="L1_3_gblup_prediction_all_2001_3000.rds")
+L1_3_gblup_prediction_all_3001_4000=readRDS(file="L1_3_gblup_prediction_all_3001_4000.rds")
+L1_3_gblup_prediction_all_4001_5000=readRDS(file="L1_3_gblup_prediction_all_4001_5000.rds")
+L1_3_gblup_prediction_all_5001_6000=readRDS(file="L1_3_gblup_prediction_all_5001_6000.rds")
+L1_3_gblup_prediction_all_6001_7000=readRDS(file="L1_3_gblup_prediction_all_6001_7000.rds")
+L1_3_gblup_prediction_all_7001_8000=readRDS(file="L1_3_gblup_prediction_all_7001_8000.rds")
+L1_3_gblup_prediction_all_8001_9000=readRDS(file="L1_3_gblup_prediction_all_8001_9000.rds")
+L1_3_gblup_prediction_all_9001_10000=readRDS(file="L1_3_gblup_prediction_all_9001_10000.rds")
+L1_3_gblup_prediction_all_10001_11000=readRDS(file="L1_3_gblup_prediction_all_10001_11000.rds")
+L1_3_gblup_prediction_all_11001_12419=readRDS(file="L1_3_gblup_prediction_all_11001_12419.rds")
+L1_3_gblup_prediction_all=c(L1_3_gblup_prediction_all_1_1000,L1_3_gblup_prediction_all_1001_2000,L1_3_gblup_prediction_all_2001_3000,L1_3_gblup_prediction_all_3001_4000,L1_3_gblup_prediction_all_4001_5000,L1_3_gblup_prediction_all_5001_6000,L1_3_gblup_prediction_all_6001_7000,L1_3_gblup_prediction_all_7001_8000,L1_3_gblup_prediction_all_8001_9000,L1_3_gblup_prediction_all_9001_10000,L1_3_gblup_prediction_all_10001_11000,L1_3_gblup_prediction_all_11001_12419)
+
+L1_3_gblup_variances_all_1_1000=readRDS(file="L1_3_gblup_variances_all_1_1000.rds")
+L1_3_gblup_variances_all_1001_2000=readRDS(file="L1_3_gblup_variances_all_1001_2000.rds")
+L1_3_gblup_variances_all_2001_3000=readRDS(file="L1_3_gblup_variances_all_2001_3000.rds")
+L1_3_gblup_variances_all_3001_4000=readRDS(file="L1_3_gblup_variances_all_3001_4000.rds")
+L1_3_gblup_variances_all_4001_5000=readRDS(file="L1_3_gblup_variances_all_4001_5000.rds")
+L1_3_gblup_variances_all_5001_6000=readRDS(file="L1_3_gblup_variances_all_5001_6000.rds")
+L1_3_gblup_variances_all_6001_7000=readRDS(file="L1_3_gblup_variances_all_6001_7000.rds")
+L1_3_gblup_variances_all_7001_8000=readRDS(file="L1_3_gblup_variances_all_7001_8000.rds")
+L1_3_gblup_variances_all_8001_9000=readRDS(file="L1_3_gblup_variances_all_8001_9000.rds")
+L1_3_gblup_variances_all_9001_10000=readRDS(file="L1_3_gblup_variances_all_9001_10000.rds")
+L1_3_gblup_variances_all_10001_11000=readRDS(file="L1_3_gblup_variances_all_10001_11000.rds")
+L1_3_gblup_variances_all_11001_12419=readRDS(file="L1_3_gblup_variances_all_11001_12419.rds")
+L1_3_gblup_variances_all=c(L1_3_gblup_variances_all_1_1000,L1_3_gblup_variances_all_1001_2000,L1_3_gblup_variances_all_2001_3000,L1_3_gblup_variances_all_3001_4000,L1_3_gblup_variances_all_4001_5000,L1_3_gblup_variances_all_5001_6000,L1_3_gblup_variances_all_6001_7000,L1_3_gblup_variances_all_7001_8000,L1_3_gblup_variances_all_8001_9000,L1_3_gblup_variances_all_9001_10000,L1_3_gblup_variances_all_10001_11000,L1_3_gblup_variances_all_11001_12419)
+
+saveRDS(L1_3_gblup_prediction_all,"L1_3_gblup_prediction_all.rds")
+saveRDS(L1_3_gblup_variances_all,"L1_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L1_3_gfblup_prediction_all_1_1000=readRDS(file="L1_3_gfblup_prediction_all_1_1000.rds")
+L1_3_gfblup_prediction_all_1001_2000=readRDS(file="L1_3_gfblup_prediction_all_1001_2000.rds")
+L1_3_gfblup_prediction_all_2001_3000=readRDS(file="L1_3_gfblup_prediction_all_2001_3000.rds")
+L1_3_gfblup_prediction_all_3001_4000=readRDS(file="L1_3_gfblup_prediction_all_3001_4000.rds")
+L1_3_gfblup_prediction_all_4001_5000=readRDS(file="L1_3_gfblup_prediction_all_4001_5000.rds")
+L1_3_gfblup_prediction_all_5001_6000=readRDS(file="L1_3_gfblup_prediction_all_5001_6000.rds")
+L1_3_gfblup_prediction_all_6001_7000=readRDS(file="L1_3_gfblup_prediction_all_6001_7000.rds")
+L1_3_gfblup_prediction_all_7001_8000=readRDS(file="L1_3_gfblup_prediction_all_7001_8000.rds")
+L1_3_gfblup_prediction_all_8001_9000=readRDS(file="L1_3_gfblup_prediction_all_8001_9000.rds")
+L1_3_gfblup_prediction_all_9001_10000=readRDS(file="L1_3_gfblup_prediction_all_9001_10000.rds")
+L1_3_gfblup_prediction_all_10001_11000=readRDS(file="L1_3_gfblup_prediction_all_10001_11000.rds")
+L1_3_gfblup_prediction_all_11001_12419=readRDS(file="L1_3_gfblup_prediction_all_11001_12419.rds")
+
+L1_3_gfblup_variances_all_1_1000=readRDS(file="L1_3_gfblup_variances_all_1_1000.rds")
+L1_3_gfblup_variances_all_1001_2000=readRDS(file="L1_3_gfblup_variances_all_1001_2000.rds")
+L1_3_gfblup_variances_all_2001_3000=readRDS(file="L1_3_gfblup_variances_all_2001_3000.rds")
+L1_3_gfblup_variances_all_3001_4000=readRDS(file="L1_3_gfblup_variances_all_3001_4000.rds")
+L1_3_gfblup_variances_all_4001_5000=readRDS(file="L1_3_gfblup_variances_all_4001_5000.rds")
+L1_3_gfblup_variances_all_5001_6000=readRDS(file="L1_3_gfblup_variances_all_5001_6000.rds")
+L1_3_gfblup_variances_all_6001_7000=readRDS(file="L1_3_gfblup_variances_all_6001_7000.rds")
+L1_3_gfblup_variances_all_7001_8000=readRDS(file="L1_3_gfblup_variances_all_7001_8000.rds")
+L1_3_gfblup_variances_all_8001_9000=readRDS(file="L1_3_gfblup_variances_all_8001_9000.rds")
+L1_3_gfblup_variances_all_9001_10000=readRDS(file="L1_3_gfblup_variances_all_9001_10000.rds")
+L1_3_gfblup_variances_all_10001_11000=readRDS(file="L1_3_gfblup_variances_all_10001_11000.rds")
+L1_3_gfblup_variances_all_11001_12419=readRDS(file="L1_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(L1_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L1_3_gfblup_variances_all=rep(list(list()),cycles)
+L1_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_1_1000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_1001_2000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_2001_3000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_3001_4000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_4001_5000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_5001_6000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_6001_7000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_7001_8000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_8001_9000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_9001_10000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_10001_11000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_11001_12419[[r]])
+
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_1_1000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_1001_2000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_2001_3000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_3001_4000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_4001_5000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_5001_6000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_6001_7000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_7001_8000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_8001_9000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_9001_10000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_10001_11000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(L1_3_gfblup_prediction_all,"L1_3_gfblup_prediction_all.rds")
+saveRDS(L1_3_gfblup_variances_all,"L1_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L2_1_gblup_prediction_all_1_1000=readRDS(file="L2_1_gblup_prediction_all_1_1000.rds")
+L2_1_gblup_prediction_all_1001_2000=readRDS(file="L2_1_gblup_prediction_all_1001_2000.rds")
+L2_1_gblup_prediction_all_2001_3000=readRDS(file="L2_1_gblup_prediction_all_2001_3000.rds")
+L2_1_gblup_prediction_all_3001_4000=readRDS(file="L2_1_gblup_prediction_all_3001_4000.rds")
+L2_1_gblup_prediction_all_4001_5000=readRDS(file="L2_1_gblup_prediction_all_4001_5000.rds")
+L2_1_gblup_prediction_all_5001_6000=readRDS(file="L2_1_gblup_prediction_all_5001_6000.rds")
+L2_1_gblup_prediction_all_6001_7000=readRDS(file="L2_1_gblup_prediction_all_6001_7000.rds")
+L2_1_gblup_prediction_all_7001_8000=readRDS(file="L2_1_gblup_prediction_all_7001_8000.rds")
+L2_1_gblup_prediction_all_8001_9000=readRDS(file="L2_1_gblup_prediction_all_8001_9000.rds")
+L2_1_gblup_prediction_all_9001_10000=readRDS(file="L2_1_gblup_prediction_all_9001_10000.rds")
+L2_1_gblup_prediction_all_10001_11000=readRDS(file="L2_1_gblup_prediction_all_10001_11000.rds")
+L2_1_gblup_prediction_all_11001_12419=readRDS(file="L2_1_gblup_prediction_all_11001_12419.rds")
+L2_1_gblup_prediction_all=c(L2_1_gblup_prediction_all_1_1000,L2_1_gblup_prediction_all_1001_2000,L2_1_gblup_prediction_all_2001_3000,L2_1_gblup_prediction_all_3001_4000,L2_1_gblup_prediction_all_4001_5000,L2_1_gblup_prediction_all_5001_6000,L2_1_gblup_prediction_all_6001_7000,L2_1_gblup_prediction_all_7001_8000,L2_1_gblup_prediction_all_8001_9000,L2_1_gblup_prediction_all_9001_10000,L2_1_gblup_prediction_all_10001_11000,L2_1_gblup_prediction_all_11001_12419)
+
+L2_1_gblup_variances_all_1_1000=readRDS(file="L2_1_gblup_variances_all_1_1000.rds")
+L2_1_gblup_variances_all_1001_2000=readRDS(file="L2_1_gblup_variances_all_1001_2000.rds")
+L2_1_gblup_variances_all_2001_3000=readRDS(file="L2_1_gblup_variances_all_2001_3000.rds")
+L2_1_gblup_variances_all_3001_4000=readRDS(file="L2_1_gblup_variances_all_3001_4000.rds")
+L2_1_gblup_variances_all_4001_5000=readRDS(file="L2_1_gblup_variances_all_4001_5000.rds")
+L2_1_gblup_variances_all_5001_6000=readRDS(file="L2_1_gblup_variances_all_5001_6000.rds")
+L2_1_gblup_variances_all_6001_7000=readRDS(file="L2_1_gblup_variances_all_6001_7000.rds")
+L2_1_gblup_variances_all_7001_8000=readRDS(file="L2_1_gblup_variances_all_7001_8000.rds")
+L2_1_gblup_variances_all_8001_9000=readRDS(file="L2_1_gblup_variances_all_8001_9000.rds")
+L2_1_gblup_variances_all_9001_10000=readRDS(file="L2_1_gblup_variances_all_9001_10000.rds")
+L2_1_gblup_variances_all_10001_11000=readRDS(file="L2_1_gblup_variances_all_10001_11000.rds")
+L2_1_gblup_variances_all_11001_12419=readRDS(file="L2_1_gblup_variances_all_11001_12419.rds")
+L2_1_gblup_variances_all=c(L2_1_gblup_variances_all_1_1000,L2_1_gblup_variances_all_1001_2000,L2_1_gblup_variances_all_2001_3000,L2_1_gblup_variances_all_3001_4000,L2_1_gblup_variances_all_4001_5000,L2_1_gblup_variances_all_5001_6000,L2_1_gblup_variances_all_6001_7000,L2_1_gblup_variances_all_7001_8000,L2_1_gblup_variances_all_8001_9000,L2_1_gblup_variances_all_9001_10000,L2_1_gblup_variances_all_10001_11000,L2_1_gblup_variances_all_11001_12419)
+
+saveRDS(L2_1_gblup_prediction_all,"L2_1_gblup_prediction_all.rds")
+saveRDS(L2_1_gblup_variances_all,"L2_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L2_1_gfblup_prediction_all_1_1000=readRDS(file="L2_1_gfblup_prediction_all_1_1000.rds")
+L2_1_gfblup_prediction_all_1001_2000=readRDS(file="L2_1_gfblup_prediction_all_1001_2000.rds")
+L2_1_gfblup_prediction_all_2001_3000=readRDS(file="L2_1_gfblup_prediction_all_2001_3000.rds")
+L2_1_gfblup_prediction_all_3001_4000=readRDS(file="L2_1_gfblup_prediction_all_3001_4000.rds")
+L2_1_gfblup_prediction_all_4001_5000=readRDS(file="L2_1_gfblup_prediction_all_4001_5000.rds")
+L2_1_gfblup_prediction_all_5001_6000=readRDS(file="L2_1_gfblup_prediction_all_5001_6000.rds")
+L2_1_gfblup_prediction_all_6001_7000=readRDS(file="L2_1_gfblup_prediction_all_6001_7000.rds")
+L2_1_gfblup_prediction_all_7001_8000=readRDS(file="L2_1_gfblup_prediction_all_7001_8000.rds")
+L2_1_gfblup_prediction_all_8001_9000=readRDS(file="L2_1_gfblup_prediction_all_8001_9000.rds")
+L2_1_gfblup_prediction_all_9001_10000=readRDS(file="L2_1_gfblup_prediction_all_9001_10000.rds")
+L2_1_gfblup_prediction_all_10001_11000=readRDS(file="L2_1_gfblup_prediction_all_10001_11000.rds")
+L2_1_gfblup_prediction_all_11001_12419=readRDS(file="L2_1_gfblup_prediction_all_11001_12419.rds")
+
+L2_1_gfblup_variances_all_1_1000=readRDS(file="L2_1_gfblup_variances_all_1_1000.rds")
+L2_1_gfblup_variances_all_1001_2000=readRDS(file="L2_1_gfblup_variances_all_1001_2000.rds")
+L2_1_gfblup_variances_all_2001_3000=readRDS(file="L2_1_gfblup_variances_all_2001_3000.rds")
+L2_1_gfblup_variances_all_3001_4000=readRDS(file="L2_1_gfblup_variances_all_3001_4000.rds")
+L2_1_gfblup_variances_all_4001_5000=readRDS(file="L2_1_gfblup_variances_all_4001_5000.rds")
+L2_1_gfblup_variances_all_5001_6000=readRDS(file="L2_1_gfblup_variances_all_5001_6000.rds")
+L2_1_gfblup_variances_all_6001_7000=readRDS(file="L2_1_gfblup_variances_all_6001_7000.rds")
+L2_1_gfblup_variances_all_7001_8000=readRDS(file="L2_1_gfblup_variances_all_7001_8000.rds")
+L2_1_gfblup_variances_all_8001_9000=readRDS(file="L2_1_gfblup_variances_all_8001_9000.rds")
+L2_1_gfblup_variances_all_9001_10000=readRDS(file="L2_1_gfblup_variances_all_9001_10000.rds")
+L2_1_gfblup_variances_all_10001_11000=readRDS(file="L2_1_gfblup_variances_all_10001_11000.rds")
+L2_1_gfblup_variances_all_11001_12419=readRDS(file="L2_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(L2_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L2_1_gfblup_variances_all=rep(list(list()),cycles)
+L2_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_1_1000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_1001_2000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_2001_3000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_3001_4000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_4001_5000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_5001_6000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_6001_7000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_7001_8000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_8001_9000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_9001_10000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_10001_11000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_11001_12419[[r]])
+
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_1_1000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_1001_2000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_2001_3000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_3001_4000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_4001_5000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_5001_6000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_6001_7000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_7001_8000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_8001_9000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_9001_10000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_10001_11000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(L2_1_gfblup_prediction_all,"L2_1_gfblup_prediction_all.rds")
+saveRDS(L2_1_gfblup_variances_all,"L2_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L2_2_gblup_prediction_all_1_1000=readRDS(file="L2_2_gblup_prediction_all_1_1000.rds")
+L2_2_gblup_prediction_all_1001_2000=readRDS(file="L2_2_gblup_prediction_all_1001_2000.rds")
+L2_2_gblup_prediction_all_2001_3000=readRDS(file="L2_2_gblup_prediction_all_2001_3000.rds")
+L2_2_gblup_prediction_all_3001_4000=readRDS(file="L2_2_gblup_prediction_all_3001_4000.rds")
+L2_2_gblup_prediction_all_4001_5000=readRDS(file="L2_2_gblup_prediction_all_4001_5000.rds")
+L2_2_gblup_prediction_all_5001_6000=readRDS(file="L2_2_gblup_prediction_all_5001_6000.rds")
+L2_2_gblup_prediction_all_6001_7000=readRDS(file="L2_2_gblup_prediction_all_6001_7000.rds")
+L2_2_gblup_prediction_all_7001_8000=readRDS(file="L2_2_gblup_prediction_all_7001_8000.rds")
+L2_2_gblup_prediction_all_8001_9000=readRDS(file="L2_2_gblup_prediction_all_8001_9000.rds")
+L2_2_gblup_prediction_all_9001_10000=readRDS(file="L2_2_gblup_prediction_all_9001_10000.rds")
+L2_2_gblup_prediction_all_10001_11000=readRDS(file="L2_2_gblup_prediction_all_10001_11000.rds")
+L2_2_gblup_prediction_all_11001_12419=readRDS(file="L2_2_gblup_prediction_all_11001_12419.rds")
+L2_2_gblup_prediction_all=c(L2_2_gblup_prediction_all_1_1000,L2_2_gblup_prediction_all_1001_2000,L2_2_gblup_prediction_all_2001_3000,L2_2_gblup_prediction_all_3001_4000,L2_2_gblup_prediction_all_4001_5000,L2_2_gblup_prediction_all_5001_6000,L2_2_gblup_prediction_all_6001_7000,L2_2_gblup_prediction_all_7001_8000,L2_2_gblup_prediction_all_8001_9000,L2_2_gblup_prediction_all_9001_10000,L2_2_gblup_prediction_all_10001_11000,L2_2_gblup_prediction_all_11001_12419)
+
+L2_2_gblup_variances_all_1_1000=readRDS(file="L2_2_gblup_variances_all_1_1000.rds")
+L2_2_gblup_variances_all_1001_2000=readRDS(file="L2_2_gblup_variances_all_1001_2000.rds")
+L2_2_gblup_variances_all_2001_3000=readRDS(file="L2_2_gblup_variances_all_2001_3000.rds")
+L2_2_gblup_variances_all_3001_4000=readRDS(file="L2_2_gblup_variances_all_3001_4000.rds")
+L2_2_gblup_variances_all_4001_5000=readRDS(file="L2_2_gblup_variances_all_4001_5000.rds")
+L2_2_gblup_variances_all_5001_6000=readRDS(file="L2_2_gblup_variances_all_5001_6000.rds")
+L2_2_gblup_variances_all_6001_7000=readRDS(file="L2_2_gblup_variances_all_6001_7000.rds")
+L2_2_gblup_variances_all_7001_8000=readRDS(file="L2_2_gblup_variances_all_7001_8000.rds")
+L2_2_gblup_variances_all_8001_9000=readRDS(file="L2_2_gblup_variances_all_8001_9000.rds")
+L2_2_gblup_variances_all_9001_10000=readRDS(file="L2_2_gblup_variances_all_9001_10000.rds")
+L2_2_gblup_variances_all_10001_11000=readRDS(file="L2_2_gblup_variances_all_10001_11000.rds")
+L2_2_gblup_variances_all_11001_12419=readRDS(file="L2_2_gblup_variances_all_11001_12419.rds")
+L2_2_gblup_variances_all=c(L2_2_gblup_variances_all_1_1000,L2_2_gblup_variances_all_1001_2000,L2_2_gblup_variances_all_2001_3000,L2_2_gblup_variances_all_3001_4000,L2_2_gblup_variances_all_4001_5000,L2_2_gblup_variances_all_5001_6000,L2_2_gblup_variances_all_6001_7000,L2_2_gblup_variances_all_7001_8000,L2_2_gblup_variances_all_8001_9000,L2_2_gblup_variances_all_9001_10000,L2_2_gblup_variances_all_10001_11000,L2_2_gblup_variances_all_11001_12419)
+
+saveRDS(L2_2_gblup_prediction_all,"L2_2_gblup_prediction_all.rds")
+saveRDS(L2_2_gblup_variances_all,"L2_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L2_2_gfblup_prediction_all_1_1000=readRDS(file="L2_2_gfblup_prediction_all_1_1000.rds")
+L2_2_gfblup_prediction_all_1001_2000=readRDS(file="L2_2_gfblup_prediction_all_1001_2000.rds")
+L2_2_gfblup_prediction_all_2001_3000=readRDS(file="L2_2_gfblup_prediction_all_2001_3000.rds")
+L2_2_gfblup_prediction_all_3001_4000=readRDS(file="L2_2_gfblup_prediction_all_3001_4000.rds")
+L2_2_gfblup_prediction_all_4001_5000=readRDS(file="L2_2_gfblup_prediction_all_4001_5000.rds")
+L2_2_gfblup_prediction_all_5001_6000=readRDS(file="L2_2_gfblup_prediction_all_5001_6000.rds")
+L2_2_gfblup_prediction_all_6001_7000=readRDS(file="L2_2_gfblup_prediction_all_6001_7000.rds")
+L2_2_gfblup_prediction_all_7001_8000=readRDS(file="L2_2_gfblup_prediction_all_7001_8000.rds")
+L2_2_gfblup_prediction_all_8001_9000=readRDS(file="L2_2_gfblup_prediction_all_8001_9000.rds")
+L2_2_gfblup_prediction_all_9001_10000=readRDS(file="L2_2_gfblup_prediction_all_9001_10000.rds")
+L2_2_gfblup_prediction_all_10001_11000=readRDS(file="L2_2_gfblup_prediction_all_10001_11000.rds")
+L2_2_gfblup_prediction_all_11001_12419=readRDS(file="L2_2_gfblup_prediction_all_11001_12419.rds")
+
+L2_2_gfblup_variances_all_1_1000=readRDS(file="L2_2_gfblup_variances_all_1_1000.rds")
+L2_2_gfblup_variances_all_1001_2000=readRDS(file="L2_2_gfblup_variances_all_1001_2000.rds")
+L2_2_gfblup_variances_all_2001_3000=readRDS(file="L2_2_gfblup_variances_all_2001_3000.rds")
+L2_2_gfblup_variances_all_3001_4000=readRDS(file="L2_2_gfblup_variances_all_3001_4000.rds")
+L2_2_gfblup_variances_all_4001_5000=readRDS(file="L2_2_gfblup_variances_all_4001_5000.rds")
+L2_2_gfblup_variances_all_5001_6000=readRDS(file="L2_2_gfblup_variances_all_5001_6000.rds")
+L2_2_gfblup_variances_all_6001_7000=readRDS(file="L2_2_gfblup_variances_all_6001_7000.rds")
+L2_2_gfblup_variances_all_7001_8000=readRDS(file="L2_2_gfblup_variances_all_7001_8000.rds")
+L2_2_gfblup_variances_all_8001_9000=readRDS(file="L2_2_gfblup_variances_all_8001_9000.rds")
+L2_2_gfblup_variances_all_9001_10000=readRDS(file="L2_2_gfblup_variances_all_9001_10000.rds")
+L2_2_gfblup_variances_all_10001_11000=readRDS(file="L2_2_gfblup_variances_all_10001_11000.rds")
+L2_2_gfblup_variances_all_11001_12419=readRDS(file="L2_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(L2_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L2_2_gfblup_variances_all=rep(list(list()),cycles)
+L2_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_1_1000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_1001_2000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_2001_3000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_3001_4000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_4001_5000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_5001_6000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_6001_7000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_7001_8000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_8001_9000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_9001_10000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_10001_11000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_11001_12419[[r]])
+
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_1_1000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_1001_2000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_2001_3000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_3001_4000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_4001_5000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_5001_6000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_6001_7000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_7001_8000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_8001_9000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_9001_10000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_10001_11000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(L2_2_gfblup_prediction_all,"L2_2_gfblup_prediction_all.rds")
+saveRDS(L2_2_gfblup_variances_all,"L2_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L2_3_gblup_prediction_all_1_1000=readRDS(file="L2_3_gblup_prediction_all_1_1000.rds")
+L2_3_gblup_prediction_all_1001_2000=readRDS(file="L2_3_gblup_prediction_all_1001_2000.rds")
+L2_3_gblup_prediction_all_2001_3000=readRDS(file="L2_3_gblup_prediction_all_2001_3000.rds")
+L2_3_gblup_prediction_all_3001_4000=readRDS(file="L2_3_gblup_prediction_all_3001_4000.rds")
+L2_3_gblup_prediction_all_4001_5000=readRDS(file="L2_3_gblup_prediction_all_4001_5000.rds")
+L2_3_gblup_prediction_all_5001_6000=readRDS(file="L2_3_gblup_prediction_all_5001_6000.rds")
+L2_3_gblup_prediction_all_6001_7000=readRDS(file="L2_3_gblup_prediction_all_6001_7000.rds")
+L2_3_gblup_prediction_all_7001_8000=readRDS(file="L2_3_gblup_prediction_all_7001_8000.rds")
+L2_3_gblup_prediction_all_8001_9000=readRDS(file="L2_3_gblup_prediction_all_8001_9000.rds")
+L2_3_gblup_prediction_all_9001_10000=readRDS(file="L2_3_gblup_prediction_all_9001_10000.rds")
+L2_3_gblup_prediction_all_10001_11000=readRDS(file="L2_3_gblup_prediction_all_10001_11000.rds")
+L2_3_gblup_prediction_all_11001_12419=readRDS(file="L2_3_gblup_prediction_all_11001_12419.rds")
+L2_3_gblup_prediction_all=c(L2_3_gblup_prediction_all_1_1000,L2_3_gblup_prediction_all_1001_2000,L2_3_gblup_prediction_all_2001_3000,L2_3_gblup_prediction_all_3001_4000,L2_3_gblup_prediction_all_4001_5000,L2_3_gblup_prediction_all_5001_6000,L2_3_gblup_prediction_all_6001_7000,L2_3_gblup_prediction_all_7001_8000,L2_3_gblup_prediction_all_8001_9000,L2_3_gblup_prediction_all_9001_10000,L2_3_gblup_prediction_all_10001_11000,L2_3_gblup_prediction_all_11001_12419)
+
+L2_3_gblup_variances_all_1_1000=readRDS(file="L2_3_gblup_variances_all_1_1000.rds")
+L2_3_gblup_variances_all_1001_2000=readRDS(file="L2_3_gblup_variances_all_1001_2000.rds")
+L2_3_gblup_variances_all_2001_3000=readRDS(file="L2_3_gblup_variances_all_2001_3000.rds")
+L2_3_gblup_variances_all_3001_4000=readRDS(file="L2_3_gblup_variances_all_3001_4000.rds")
+L2_3_gblup_variances_all_4001_5000=readRDS(file="L2_3_gblup_variances_all_4001_5000.rds")
+L2_3_gblup_variances_all_5001_6000=readRDS(file="L2_3_gblup_variances_all_5001_6000.rds")
+L2_3_gblup_variances_all_6001_7000=readRDS(file="L2_3_gblup_variances_all_6001_7000.rds")
+L2_3_gblup_variances_all_7001_8000=readRDS(file="L2_3_gblup_variances_all_7001_8000.rds")
+L2_3_gblup_variances_all_8001_9000=readRDS(file="L2_3_gblup_variances_all_8001_9000.rds")
+L2_3_gblup_variances_all_9001_10000=readRDS(file="L2_3_gblup_variances_all_9001_10000.rds")
+L2_3_gblup_variances_all_10001_11000=readRDS(file="L2_3_gblup_variances_all_10001_11000.rds")
+L2_3_gblup_variances_all_11001_12419=readRDS(file="L2_3_gblup_variances_all_11001_12419.rds")
+L2_3_gblup_variances_all=c(L2_3_gblup_variances_all_1_1000,L2_3_gblup_variances_all_1001_2000,L2_3_gblup_variances_all_2001_3000,L2_3_gblup_variances_all_3001_4000,L2_3_gblup_variances_all_4001_5000,L2_3_gblup_variances_all_5001_6000,L2_3_gblup_variances_all_6001_7000,L2_3_gblup_variances_all_7001_8000,L2_3_gblup_variances_all_8001_9000,L2_3_gblup_variances_all_9001_10000,L2_3_gblup_variances_all_10001_11000,L2_3_gblup_variances_all_11001_12419)
+
+saveRDS(L2_3_gblup_prediction_all,"L2_3_gblup_prediction_all.rds")
+saveRDS(L2_3_gblup_variances_all,"L2_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L2_3_gfblup_prediction_all_1_1000=readRDS(file="L2_3_gfblup_prediction_all_1_1000.rds")
+L2_3_gfblup_prediction_all_1001_2000=readRDS(file="L2_3_gfblup_prediction_all_1001_2000.rds")
+L2_3_gfblup_prediction_all_2001_3000=readRDS(file="L2_3_gfblup_prediction_all_2001_3000.rds")
+L2_3_gfblup_prediction_all_3001_4000=readRDS(file="L2_3_gfblup_prediction_all_3001_4000.rds")
+L2_3_gfblup_prediction_all_4001_5000=readRDS(file="L2_3_gfblup_prediction_all_4001_5000.rds")
+L2_3_gfblup_prediction_all_5001_6000=readRDS(file="L2_3_gfblup_prediction_all_5001_6000.rds")
+L2_3_gfblup_prediction_all_6001_7000=readRDS(file="L2_3_gfblup_prediction_all_6001_7000.rds")
+L2_3_gfblup_prediction_all_7001_8000=readRDS(file="L2_3_gfblup_prediction_all_7001_8000.rds")
+L2_3_gfblup_prediction_all_8001_9000=readRDS(file="L2_3_gfblup_prediction_all_8001_9000.rds")
+L2_3_gfblup_prediction_all_9001_10000=readRDS(file="L2_3_gfblup_prediction_all_9001_10000.rds")
+L2_3_gfblup_prediction_all_10001_11000=readRDS(file="L2_3_gfblup_prediction_all_10001_11000.rds")
+L2_3_gfblup_prediction_all_11001_12419=readRDS(file="L2_3_gfblup_prediction_all_11001_12419.rds")
+
+L2_3_gfblup_variances_all_1_1000=readRDS(file="L2_3_gfblup_variances_all_1_1000.rds")
+L2_3_gfblup_variances_all_1001_2000=readRDS(file="L2_3_gfblup_variances_all_1001_2000.rds")
+L2_3_gfblup_variances_all_2001_3000=readRDS(file="L2_3_gfblup_variances_all_2001_3000.rds")
+L2_3_gfblup_variances_all_3001_4000=readRDS(file="L2_3_gfblup_variances_all_3001_4000.rds")
+L2_3_gfblup_variances_all_4001_5000=readRDS(file="L2_3_gfblup_variances_all_4001_5000.rds")
+L2_3_gfblup_variances_all_5001_6000=readRDS(file="L2_3_gfblup_variances_all_5001_6000.rds")
+L2_3_gfblup_variances_all_6001_7000=readRDS(file="L2_3_gfblup_variances_all_6001_7000.rds")
+L2_3_gfblup_variances_all_7001_8000=readRDS(file="L2_3_gfblup_variances_all_7001_8000.rds")
+L2_3_gfblup_variances_all_8001_9000=readRDS(file="L2_3_gfblup_variances_all_8001_9000.rds")
+L2_3_gfblup_variances_all_9001_10000=readRDS(file="L2_3_gfblup_variances_all_9001_10000.rds")
+L2_3_gfblup_variances_all_10001_11000=readRDS(file="L2_3_gfblup_variances_all_10001_11000.rds")
+L2_3_gfblup_variances_all_11001_12419=readRDS(file="L2_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(L2_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L2_3_gfblup_variances_all=rep(list(list()),cycles)
+L2_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_1_1000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_1001_2000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_2001_3000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_3001_4000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_4001_5000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_5001_6000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_6001_7000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_7001_8000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_8001_9000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_9001_10000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_10001_11000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_11001_12419[[r]])
+
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_1_1000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_1001_2000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_2001_3000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_3001_4000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_4001_5000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_5001_6000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_6001_7000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_7001_8000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_8001_9000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_9001_10000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_10001_11000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(L2_3_gfblup_prediction_all,"L2_3_gfblup_prediction_all.rds")
+saveRDS(L2_3_gfblup_variances_all,"L2_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H1_1_gblup_prediction_all_1_1000=readRDS(file="H1_1_gblup_prediction_all_1_1000.rds")
+H1_1_gblup_prediction_all_1001_2000=readRDS(file="H1_1_gblup_prediction_all_1001_2000.rds")
+H1_1_gblup_prediction_all_2001_3000=readRDS(file="H1_1_gblup_prediction_all_2001_3000.rds")
+H1_1_gblup_prediction_all_3001_4000=readRDS(file="H1_1_gblup_prediction_all_3001_4000.rds")
+H1_1_gblup_prediction_all_4001_5000=readRDS(file="H1_1_gblup_prediction_all_4001_5000.rds")
+H1_1_gblup_prediction_all_5001_6000=readRDS(file="H1_1_gblup_prediction_all_5001_6000.rds")
+H1_1_gblup_prediction_all_6001_7000=readRDS(file="H1_1_gblup_prediction_all_6001_7000.rds")
+H1_1_gblup_prediction_all_7001_8000=readRDS(file="H1_1_gblup_prediction_all_7001_8000.rds")
+H1_1_gblup_prediction_all_8001_9000=readRDS(file="H1_1_gblup_prediction_all_8001_9000.rds")
+H1_1_gblup_prediction_all_9001_10000=readRDS(file="H1_1_gblup_prediction_all_9001_10000.rds")
+H1_1_gblup_prediction_all_10001_11000=readRDS(file="H1_1_gblup_prediction_all_10001_11000.rds")
+H1_1_gblup_prediction_all_11001_12419=readRDS(file="H1_1_gblup_prediction_all_11001_12419.rds")
+H1_1_gblup_prediction_all=c(H1_1_gblup_prediction_all_1_1000,H1_1_gblup_prediction_all_1001_2000,H1_1_gblup_prediction_all_2001_3000,H1_1_gblup_prediction_all_3001_4000,H1_1_gblup_prediction_all_4001_5000,H1_1_gblup_prediction_all_5001_6000,H1_1_gblup_prediction_all_6001_7000,H1_1_gblup_prediction_all_7001_8000,H1_1_gblup_prediction_all_8001_9000,H1_1_gblup_prediction_all_9001_10000,H1_1_gblup_prediction_all_10001_11000,H1_1_gblup_prediction_all_11001_12419)
+
+H1_1_gblup_variances_all_1_1000=readRDS(file="H1_1_gblup_variances_all_1_1000.rds")
+H1_1_gblup_variances_all_1001_2000=readRDS(file="H1_1_gblup_variances_all_1001_2000.rds")
+H1_1_gblup_variances_all_2001_3000=readRDS(file="H1_1_gblup_variances_all_2001_3000.rds")
+H1_1_gblup_variances_all_3001_4000=readRDS(file="H1_1_gblup_variances_all_3001_4000.rds")
+H1_1_gblup_variances_all_4001_5000=readRDS(file="H1_1_gblup_variances_all_4001_5000.rds")
+H1_1_gblup_variances_all_5001_6000=readRDS(file="H1_1_gblup_variances_all_5001_6000.rds")
+H1_1_gblup_variances_all_6001_7000=readRDS(file="H1_1_gblup_variances_all_6001_7000.rds")
+H1_1_gblup_variances_all_7001_8000=readRDS(file="H1_1_gblup_variances_all_7001_8000.rds")
+H1_1_gblup_variances_all_8001_9000=readRDS(file="H1_1_gblup_variances_all_8001_9000.rds")
+H1_1_gblup_variances_all_9001_10000=readRDS(file="H1_1_gblup_variances_all_9001_10000.rds")
+H1_1_gblup_variances_all_10001_11000=readRDS(file="H1_1_gblup_variances_all_10001_11000.rds")
+H1_1_gblup_variances_all_11001_12419=readRDS(file="H1_1_gblup_variances_all_11001_12419.rds")
+H1_1_gblup_variances_all=c(H1_1_gblup_variances_all_1_1000,H1_1_gblup_variances_all_1001_2000,H1_1_gblup_variances_all_2001_3000,H1_1_gblup_variances_all_3001_4000,H1_1_gblup_variances_all_4001_5000,H1_1_gblup_variances_all_5001_6000,H1_1_gblup_variances_all_6001_7000,H1_1_gblup_variances_all_7001_8000,H1_1_gblup_variances_all_8001_9000,H1_1_gblup_variances_all_9001_10000,H1_1_gblup_variances_all_10001_11000,H1_1_gblup_variances_all_11001_12419)
+
+saveRDS(H1_1_gblup_prediction_all,"H1_1_gblup_prediction_all.rds")
+saveRDS(H1_1_gblup_variances_all,"H1_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H1_1_gfblup_prediction_all_1_1000=readRDS(file="H1_1_gfblup_prediction_all_1_1000.rds")
+H1_1_gfblup_prediction_all_1001_2000=readRDS(file="H1_1_gfblup_prediction_all_1001_2000.rds")
+H1_1_gfblup_prediction_all_2001_3000=readRDS(file="H1_1_gfblup_prediction_all_2001_3000.rds")
+H1_1_gfblup_prediction_all_3001_4000=readRDS(file="H1_1_gfblup_prediction_all_3001_4000.rds")
+H1_1_gfblup_prediction_all_4001_5000=readRDS(file="H1_1_gfblup_prediction_all_4001_5000.rds")
+H1_1_gfblup_prediction_all_5001_6000=readRDS(file="H1_1_gfblup_prediction_all_5001_6000.rds")
+H1_1_gfblup_prediction_all_6001_7000=readRDS(file="H1_1_gfblup_prediction_all_6001_7000.rds")
+H1_1_gfblup_prediction_all_7001_8000=readRDS(file="H1_1_gfblup_prediction_all_7001_8000.rds")
+H1_1_gfblup_prediction_all_8001_9000=readRDS(file="H1_1_gfblup_prediction_all_8001_9000.rds")
+H1_1_gfblup_prediction_all_9001_10000=readRDS(file="H1_1_gfblup_prediction_all_9001_10000.rds")
+H1_1_gfblup_prediction_all_10001_11000=readRDS(file="H1_1_gfblup_prediction_all_10001_11000.rds")
+H1_1_gfblup_prediction_all_11001_12419=readRDS(file="H1_1_gfblup_prediction_all_11001_12419.rds")
+
+H1_1_gfblup_variances_all_1_1000=readRDS(file="H1_1_gfblup_variances_all_1_1000.rds")
+H1_1_gfblup_variances_all_1001_2000=readRDS(file="H1_1_gfblup_variances_all_1001_2000.rds")
+H1_1_gfblup_variances_all_2001_3000=readRDS(file="H1_1_gfblup_variances_all_2001_3000.rds")
+H1_1_gfblup_variances_all_3001_4000=readRDS(file="H1_1_gfblup_variances_all_3001_4000.rds")
+H1_1_gfblup_variances_all_4001_5000=readRDS(file="H1_1_gfblup_variances_all_4001_5000.rds")
+H1_1_gfblup_variances_all_5001_6000=readRDS(file="H1_1_gfblup_variances_all_5001_6000.rds")
+H1_1_gfblup_variances_all_6001_7000=readRDS(file="H1_1_gfblup_variances_all_6001_7000.rds")
+H1_1_gfblup_variances_all_7001_8000=readRDS(file="H1_1_gfblup_variances_all_7001_8000.rds")
+H1_1_gfblup_variances_all_8001_9000=readRDS(file="H1_1_gfblup_variances_all_8001_9000.rds")
+H1_1_gfblup_variances_all_9001_10000=readRDS(file="H1_1_gfblup_variances_all_9001_10000.rds")
+H1_1_gfblup_variances_all_10001_11000=readRDS(file="H1_1_gfblup_variances_all_10001_11000.rds")
+H1_1_gfblup_variances_all_11001_12419=readRDS(file="H1_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H1_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H1_1_gfblup_variances_all=rep(list(list()),cycles)
+H1_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_1_1000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_1001_2000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_2001_3000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_3001_4000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_4001_5000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_5001_6000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_6001_7000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_7001_8000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_8001_9000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_9001_10000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_10001_11000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_11001_12419[[r]])
+
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_1_1000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_1001_2000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_2001_3000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_3001_4000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_4001_5000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_5001_6000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_6001_7000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_7001_8000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_8001_9000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_9001_10000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_10001_11000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H1_1_gfblup_prediction_all,"H1_1_gfblup_prediction_all.rds")
+saveRDS(H1_1_gfblup_variances_all,"H1_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H1_2_gblup_prediction_all_1_1000=readRDS(file="H1_2_gblup_prediction_all_1_1000.rds")
+H1_2_gblup_prediction_all_1001_2000=readRDS(file="H1_2_gblup_prediction_all_1001_2000.rds")
+H1_2_gblup_prediction_all_2001_3000=readRDS(file="H1_2_gblup_prediction_all_2001_3000.rds")
+H1_2_gblup_prediction_all_3001_4000=readRDS(file="H1_2_gblup_prediction_all_3001_4000.rds")
+H1_2_gblup_prediction_all_4001_5000=readRDS(file="H1_2_gblup_prediction_all_4001_5000.rds")
+H1_2_gblup_prediction_all_5001_6000=readRDS(file="H1_2_gblup_prediction_all_5001_6000.rds")
+H1_2_gblup_prediction_all_6001_7000=readRDS(file="H1_2_gblup_prediction_all_6001_7000.rds")
+H1_2_gblup_prediction_all_7001_8000=readRDS(file="H1_2_gblup_prediction_all_7001_8000.rds")
+H1_2_gblup_prediction_all_8001_9000=readRDS(file="H1_2_gblup_prediction_all_8001_9000.rds")
+H1_2_gblup_prediction_all_9001_10000=readRDS(file="H1_2_gblup_prediction_all_9001_10000.rds")
+H1_2_gblup_prediction_all_10001_11000=readRDS(file="H1_2_gblup_prediction_all_10001_11000.rds")
+H1_2_gblup_prediction_all_11001_12419=readRDS(file="H1_2_gblup_prediction_all_11001_12419.rds")
+H1_2_gblup_prediction_all=c(H1_2_gblup_prediction_all_1_1000,H1_2_gblup_prediction_all_1001_2000,H1_2_gblup_prediction_all_2001_3000,H1_2_gblup_prediction_all_3001_4000,H1_2_gblup_prediction_all_4001_5000,H1_2_gblup_prediction_all_5001_6000,H1_2_gblup_prediction_all_6001_7000,H1_2_gblup_prediction_all_7001_8000,H1_2_gblup_prediction_all_8001_9000,H1_2_gblup_prediction_all_9001_10000,H1_2_gblup_prediction_all_10001_11000,H1_2_gblup_prediction_all_11001_12419)
+
+H1_2_gblup_variances_all_1_1000=readRDS(file="H1_2_gblup_variances_all_1_1000.rds")
+H1_2_gblup_variances_all_1001_2000=readRDS(file="H1_2_gblup_variances_all_1001_2000.rds")
+H1_2_gblup_variances_all_2001_3000=readRDS(file="H1_2_gblup_variances_all_2001_3000.rds")
+H1_2_gblup_variances_all_3001_4000=readRDS(file="H1_2_gblup_variances_all_3001_4000.rds")
+H1_2_gblup_variances_all_4001_5000=readRDS(file="H1_2_gblup_variances_all_4001_5000.rds")
+H1_2_gblup_variances_all_5001_6000=readRDS(file="H1_2_gblup_variances_all_5001_6000.rds")
+H1_2_gblup_variances_all_6001_7000=readRDS(file="H1_2_gblup_variances_all_6001_7000.rds")
+H1_2_gblup_variances_all_7001_8000=readRDS(file="H1_2_gblup_variances_all_7001_8000.rds")
+H1_2_gblup_variances_all_8001_9000=readRDS(file="H1_2_gblup_variances_all_8001_9000.rds")
+H1_2_gblup_variances_all_9001_10000=readRDS(file="H1_2_gblup_variances_all_9001_10000.rds")
+H1_2_gblup_variances_all_10001_11000=readRDS(file="H1_2_gblup_variances_all_10001_11000.rds")
+H1_2_gblup_variances_all_11001_12419=readRDS(file="H1_2_gblup_variances_all_11001_12419.rds")
+H1_2_gblup_variances_all=c(H1_2_gblup_variances_all_1_1000,H1_2_gblup_variances_all_1001_2000,H1_2_gblup_variances_all_2001_3000,H1_2_gblup_variances_all_3001_4000,H1_2_gblup_variances_all_4001_5000,H1_2_gblup_variances_all_5001_6000,H1_2_gblup_variances_all_6001_7000,H1_2_gblup_variances_all_7001_8000,H1_2_gblup_variances_all_8001_9000,H1_2_gblup_variances_all_9001_10000,H1_2_gblup_variances_all_10001_11000,H1_2_gblup_variances_all_11001_12419)
+
+saveRDS(H1_2_gblup_prediction_all,"H1_2_gblup_prediction_all.rds")
+saveRDS(H1_2_gblup_variances_all,"H1_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H1_2_gfblup_prediction_all_1_1000=readRDS(file="H1_2_gfblup_prediction_all_1_1000.rds")
+H1_2_gfblup_prediction_all_1001_2000=readRDS(file="H1_2_gfblup_prediction_all_1001_2000.rds")
+H1_2_gfblup_prediction_all_2001_3000=readRDS(file="H1_2_gfblup_prediction_all_2001_3000.rds")
+H1_2_gfblup_prediction_all_3001_4000=readRDS(file="H1_2_gfblup_prediction_all_3001_4000.rds")
+H1_2_gfblup_prediction_all_4001_5000=readRDS(file="H1_2_gfblup_prediction_all_4001_5000.rds")
+H1_2_gfblup_prediction_all_5001_6000=readRDS(file="H1_2_gfblup_prediction_all_5001_6000.rds")
+H1_2_gfblup_prediction_all_6001_7000=readRDS(file="H1_2_gfblup_prediction_all_6001_7000.rds")
+H1_2_gfblup_prediction_all_7001_8000=readRDS(file="H1_2_gfblup_prediction_all_7001_8000.rds")
+H1_2_gfblup_prediction_all_8001_9000=readRDS(file="H1_2_gfblup_prediction_all_8001_9000.rds")
+H1_2_gfblup_prediction_all_9001_10000=readRDS(file="H1_2_gfblup_prediction_all_9001_10000.rds")
+H1_2_gfblup_prediction_all_10001_11000=readRDS(file="H1_2_gfblup_prediction_all_10001_11000.rds")
+H1_2_gfblup_prediction_all_11001_12419=readRDS(file="H1_2_gfblup_prediction_all_11001_12419.rds")
+
+H1_2_gfblup_variances_all_1_1000=readRDS(file="H1_2_gfblup_variances_all_1_1000.rds")
+H1_2_gfblup_variances_all_1001_2000=readRDS(file="H1_2_gfblup_variances_all_1001_2000.rds")
+H1_2_gfblup_variances_all_2001_3000=readRDS(file="H1_2_gfblup_variances_all_2001_3000.rds")
+H1_2_gfblup_variances_all_3001_4000=readRDS(file="H1_2_gfblup_variances_all_3001_4000.rds")
+H1_2_gfblup_variances_all_4001_5000=readRDS(file="H1_2_gfblup_variances_all_4001_5000.rds")
+H1_2_gfblup_variances_all_5001_6000=readRDS(file="H1_2_gfblup_variances_all_5001_6000.rds")
+H1_2_gfblup_variances_all_6001_7000=readRDS(file="H1_2_gfblup_variances_all_6001_7000.rds")
+H1_2_gfblup_variances_all_7001_8000=readRDS(file="H1_2_gfblup_variances_all_7001_8000.rds")
+H1_2_gfblup_variances_all_8001_9000=readRDS(file="H1_2_gfblup_variances_all_8001_9000.rds")
+H1_2_gfblup_variances_all_9001_10000=readRDS(file="H1_2_gfblup_variances_all_9001_10000.rds")
+H1_2_gfblup_variances_all_10001_11000=readRDS(file="H1_2_gfblup_variances_all_10001_11000.rds")
+H1_2_gfblup_variances_all_11001_12419=readRDS(file="H1_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H1_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H1_2_gfblup_variances_all=rep(list(list()),cycles)
+H1_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_1_1000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_1001_2000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_2001_3000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_3001_4000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_4001_5000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_5001_6000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_6001_7000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_7001_8000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_8001_9000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_9001_10000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_10001_11000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_11001_12419[[r]])
+
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_1_1000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_1001_2000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_2001_3000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_3001_4000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_4001_5000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_5001_6000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_6001_7000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_7001_8000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_8001_9000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_9001_10000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_10001_11000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H1_2_gfblup_prediction_all,"H1_2_gfblup_prediction_all.rds")
+saveRDS(H1_2_gfblup_variances_all,"H1_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H1_3_gblup_prediction_all_1_1000=readRDS(file="H1_3_gblup_prediction_all_1_1000.rds")
+H1_3_gblup_prediction_all_1001_2000=readRDS(file="H1_3_gblup_prediction_all_1001_2000.rds")
+H1_3_gblup_prediction_all_2001_3000=readRDS(file="H1_3_gblup_prediction_all_2001_3000.rds")
+H1_3_gblup_prediction_all_3001_4000=readRDS(file="H1_3_gblup_prediction_all_3001_4000.rds")
+H1_3_gblup_prediction_all_4001_5000=readRDS(file="H1_3_gblup_prediction_all_4001_5000.rds")
+H1_3_gblup_prediction_all_5001_6000=readRDS(file="H1_3_gblup_prediction_all_5001_6000.rds")
+H1_3_gblup_prediction_all_6001_7000=readRDS(file="H1_3_gblup_prediction_all_6001_7000.rds")
+H1_3_gblup_prediction_all_7001_8000=readRDS(file="H1_3_gblup_prediction_all_7001_8000.rds")
+H1_3_gblup_prediction_all_8001_9000=readRDS(file="H1_3_gblup_prediction_all_8001_9000.rds")
+H1_3_gblup_prediction_all_9001_10000=readRDS(file="H1_3_gblup_prediction_all_9001_10000.rds")
+H1_3_gblup_prediction_all_10001_11000=readRDS(file="H1_3_gblup_prediction_all_10001_11000.rds")
+H1_3_gblup_prediction_all_11001_12419=readRDS(file="H1_3_gblup_prediction_all_11001_12419.rds")
+H1_3_gblup_prediction_all=c(H1_3_gblup_prediction_all_1_1000,H1_3_gblup_prediction_all_1001_2000,H1_3_gblup_prediction_all_2001_3000,H1_3_gblup_prediction_all_3001_4000,H1_3_gblup_prediction_all_4001_5000,H1_3_gblup_prediction_all_5001_6000,H1_3_gblup_prediction_all_6001_7000,H1_3_gblup_prediction_all_7001_8000,H1_3_gblup_prediction_all_8001_9000,H1_3_gblup_prediction_all_9001_10000,H1_3_gblup_prediction_all_10001_11000,H1_3_gblup_prediction_all_11001_12419)
+
+H1_3_gblup_variances_all_1_1000=readRDS(file="H1_3_gblup_variances_all_1_1000.rds")
+H1_3_gblup_variances_all_1001_2000=readRDS(file="H1_3_gblup_variances_all_1001_2000.rds")
+H1_3_gblup_variances_all_2001_3000=readRDS(file="H1_3_gblup_variances_all_2001_3000.rds")
+H1_3_gblup_variances_all_3001_4000=readRDS(file="H1_3_gblup_variances_all_3001_4000.rds")
+H1_3_gblup_variances_all_4001_5000=readRDS(file="H1_3_gblup_variances_all_4001_5000.rds")
+H1_3_gblup_variances_all_5001_6000=readRDS(file="H1_3_gblup_variances_all_5001_6000.rds")
+H1_3_gblup_variances_all_6001_7000=readRDS(file="H1_3_gblup_variances_all_6001_7000.rds")
+H1_3_gblup_variances_all_7001_8000=readRDS(file="H1_3_gblup_variances_all_7001_8000.rds")
+H1_3_gblup_variances_all_8001_9000=readRDS(file="H1_3_gblup_variances_all_8001_9000.rds")
+H1_3_gblup_variances_all_9001_10000=readRDS(file="H1_3_gblup_variances_all_9001_10000.rds")
+H1_3_gblup_variances_all_10001_11000=readRDS(file="H1_3_gblup_variances_all_10001_11000.rds")
+H1_3_gblup_variances_all_11001_12419=readRDS(file="H1_3_gblup_variances_all_11001_12419.rds")
+H1_3_gblup_variances_all=c(H1_3_gblup_variances_all_1_1000,H1_3_gblup_variances_all_1001_2000,H1_3_gblup_variances_all_2001_3000,H1_3_gblup_variances_all_3001_4000,H1_3_gblup_variances_all_4001_5000,H1_3_gblup_variances_all_5001_6000,H1_3_gblup_variances_all_6001_7000,H1_3_gblup_variances_all_7001_8000,H1_3_gblup_variances_all_8001_9000,H1_3_gblup_variances_all_9001_10000,H1_3_gblup_variances_all_10001_11000,H1_3_gblup_variances_all_11001_12419)
+
+saveRDS(H1_3_gblup_prediction_all,"H1_3_gblup_prediction_all.rds")
+saveRDS(H1_3_gblup_variances_all,"H1_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H1_3_gfblup_prediction_all_1_1000=readRDS(file="H1_3_gfblup_prediction_all_1_1000.rds")
+H1_3_gfblup_prediction_all_1001_2000=readRDS(file="H1_3_gfblup_prediction_all_1001_2000.rds")
+H1_3_gfblup_prediction_all_2001_3000=readRDS(file="H1_3_gfblup_prediction_all_2001_3000.rds")
+H1_3_gfblup_prediction_all_3001_4000=readRDS(file="H1_3_gfblup_prediction_all_3001_4000.rds")
+H1_3_gfblup_prediction_all_4001_5000=readRDS(file="H1_3_gfblup_prediction_all_4001_5000.rds")
+H1_3_gfblup_prediction_all_5001_6000=readRDS(file="H1_3_gfblup_prediction_all_5001_6000.rds")
+H1_3_gfblup_prediction_all_6001_7000=readRDS(file="H1_3_gfblup_prediction_all_6001_7000.rds")
+H1_3_gfblup_prediction_all_7001_8000=readRDS(file="H1_3_gfblup_prediction_all_7001_8000.rds")
+H1_3_gfblup_prediction_all_8001_9000=readRDS(file="H1_3_gfblup_prediction_all_8001_9000.rds")
+H1_3_gfblup_prediction_all_9001_10000=readRDS(file="H1_3_gfblup_prediction_all_9001_10000.rds")
+H1_3_gfblup_prediction_all_10001_11000=readRDS(file="H1_3_gfblup_prediction_all_10001_11000.rds")
+H1_3_gfblup_prediction_all_11001_12419=readRDS(file="H1_3_gfblup_prediction_all_11001_12419.rds")
+
+H1_3_gfblup_variances_all_1_1000=readRDS(file="H1_3_gfblup_variances_all_1_1000.rds")
+H1_3_gfblup_variances_all_1001_2000=readRDS(file="H1_3_gfblup_variances_all_1001_2000.rds")
+H1_3_gfblup_variances_all_2001_3000=readRDS(file="H1_3_gfblup_variances_all_2001_3000.rds")
+H1_3_gfblup_variances_all_3001_4000=readRDS(file="H1_3_gfblup_variances_all_3001_4000.rds")
+H1_3_gfblup_variances_all_4001_5000=readRDS(file="H1_3_gfblup_variances_all_4001_5000.rds")
+H1_3_gfblup_variances_all_5001_6000=readRDS(file="H1_3_gfblup_variances_all_5001_6000.rds")
+H1_3_gfblup_variances_all_6001_7000=readRDS(file="H1_3_gfblup_variances_all_6001_7000.rds")
+H1_3_gfblup_variances_all_7001_8000=readRDS(file="H1_3_gfblup_variances_all_7001_8000.rds")
+H1_3_gfblup_variances_all_8001_9000=readRDS(file="H1_3_gfblup_variances_all_8001_9000.rds")
+H1_3_gfblup_variances_all_9001_10000=readRDS(file="H1_3_gfblup_variances_all_9001_10000.rds")
+H1_3_gfblup_variances_all_10001_11000=readRDS(file="H1_3_gfblup_variances_all_10001_11000.rds")
+H1_3_gfblup_variances_all_11001_12419=readRDS(file="H1_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H1_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H1_3_gfblup_variances_all=rep(list(list()),cycles)
+H1_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_1_1000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_1001_2000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_2001_3000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_3001_4000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_4001_5000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_5001_6000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_6001_7000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_7001_8000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_8001_9000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_9001_10000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_10001_11000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_11001_12419[[r]])
+
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_1_1000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_1001_2000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_2001_3000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_3001_4000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_4001_5000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_5001_6000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_6001_7000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_7001_8000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_8001_9000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_9001_10000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_10001_11000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H1_3_gfblup_prediction_all,"H1_3_gfblup_prediction_all.rds")
+saveRDS(H1_3_gfblup_variances_all,"H1_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H2_1_gblup_prediction_all_1_1000=readRDS(file="H2_1_gblup_prediction_all_1_1000.rds")
+H2_1_gblup_prediction_all_1001_2000=readRDS(file="H2_1_gblup_prediction_all_1001_2000.rds")
+H2_1_gblup_prediction_all_2001_3000=readRDS(file="H2_1_gblup_prediction_all_2001_3000.rds")
+H2_1_gblup_prediction_all_3001_4000=readRDS(file="H2_1_gblup_prediction_all_3001_4000.rds")
+H2_1_gblup_prediction_all_4001_5000=readRDS(file="H2_1_gblup_prediction_all_4001_5000.rds")
+H2_1_gblup_prediction_all_5001_6000=readRDS(file="H2_1_gblup_prediction_all_5001_6000.rds")
+H2_1_gblup_prediction_all_6001_7000=readRDS(file="H2_1_gblup_prediction_all_6001_7000.rds")
+H2_1_gblup_prediction_all_7001_8000=readRDS(file="H2_1_gblup_prediction_all_7001_8000.rds")
+H2_1_gblup_prediction_all_8001_9000=readRDS(file="H2_1_gblup_prediction_all_8001_9000.rds")
+H2_1_gblup_prediction_all_9001_10000=readRDS(file="H2_1_gblup_prediction_all_9001_10000.rds")
+H2_1_gblup_prediction_all_10001_11000=readRDS(file="H2_1_gblup_prediction_all_10001_11000.rds")
+H2_1_gblup_prediction_all_11001_12419=readRDS(file="H2_1_gblup_prediction_all_11001_12419.rds")
+H2_1_gblup_prediction_all=c(H2_1_gblup_prediction_all_1_1000,H2_1_gblup_prediction_all_1001_2000,H2_1_gblup_prediction_all_2001_3000,H2_1_gblup_prediction_all_3001_4000,H2_1_gblup_prediction_all_4001_5000,H2_1_gblup_prediction_all_5001_6000,H2_1_gblup_prediction_all_6001_7000,H2_1_gblup_prediction_all_7001_8000,H2_1_gblup_prediction_all_8001_9000,H2_1_gblup_prediction_all_9001_10000,H2_1_gblup_prediction_all_10001_11000,H2_1_gblup_prediction_all_11001_12419)
+
+H2_1_gblup_variances_all_1_1000=readRDS(file="H2_1_gblup_variances_all_1_1000.rds")
+H2_1_gblup_variances_all_1001_2000=readRDS(file="H2_1_gblup_variances_all_1001_2000.rds")
+H2_1_gblup_variances_all_2001_3000=readRDS(file="H2_1_gblup_variances_all_2001_3000.rds")
+H2_1_gblup_variances_all_3001_4000=readRDS(file="H2_1_gblup_variances_all_3001_4000.rds")
+H2_1_gblup_variances_all_4001_5000=readRDS(file="H2_1_gblup_variances_all_4001_5000.rds")
+H2_1_gblup_variances_all_5001_6000=readRDS(file="H2_1_gblup_variances_all_5001_6000.rds")
+H2_1_gblup_variances_all_6001_7000=readRDS(file="H2_1_gblup_variances_all_6001_7000.rds")
+H2_1_gblup_variances_all_7001_8000=readRDS(file="H2_1_gblup_variances_all_7001_8000.rds")
+H2_1_gblup_variances_all_8001_9000=readRDS(file="H2_1_gblup_variances_all_8001_9000.rds")
+H2_1_gblup_variances_all_9001_10000=readRDS(file="H2_1_gblup_variances_all_9001_10000.rds")
+H2_1_gblup_variances_all_10001_11000=readRDS(file="H2_1_gblup_variances_all_10001_11000.rds")
+H2_1_gblup_variances_all_11001_12419=readRDS(file="H2_1_gblup_variances_all_11001_12419.rds")
+H2_1_gblup_variances_all=c(H2_1_gblup_variances_all_1_1000,H2_1_gblup_variances_all_1001_2000,H2_1_gblup_variances_all_2001_3000,H2_1_gblup_variances_all_3001_4000,H2_1_gblup_variances_all_4001_5000,H2_1_gblup_variances_all_5001_6000,H2_1_gblup_variances_all_6001_7000,H2_1_gblup_variances_all_7001_8000,H2_1_gblup_variances_all_8001_9000,H2_1_gblup_variances_all_9001_10000,H2_1_gblup_variances_all_10001_11000,H2_1_gblup_variances_all_11001_12419)
+
+saveRDS(H2_1_gblup_prediction_all,"H2_1_gblup_prediction_all.rds")
+saveRDS(H2_1_gblup_variances_all,"H2_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H2_1_gfblup_prediction_all_1_1000=readRDS(file="H2_1_gfblup_prediction_all_1_1000.rds")
+H2_1_gfblup_prediction_all_1001_2000=readRDS(file="H2_1_gfblup_prediction_all_1001_2000.rds")
+H2_1_gfblup_prediction_all_2001_3000=readRDS(file="H2_1_gfblup_prediction_all_2001_3000.rds")
+H2_1_gfblup_prediction_all_3001_4000=readRDS(file="H2_1_gfblup_prediction_all_3001_4000.rds")
+H2_1_gfblup_prediction_all_4001_5000=readRDS(file="H2_1_gfblup_prediction_all_4001_5000.rds")
+H2_1_gfblup_prediction_all_5001_6000=readRDS(file="H2_1_gfblup_prediction_all_5001_6000.rds")
+H2_1_gfblup_prediction_all_6001_7000=readRDS(file="H2_1_gfblup_prediction_all_6001_7000.rds")
+H2_1_gfblup_prediction_all_7001_8000=readRDS(file="H2_1_gfblup_prediction_all_7001_8000.rds")
+H2_1_gfblup_prediction_all_8001_9000=readRDS(file="H2_1_gfblup_prediction_all_8001_9000.rds")
+H2_1_gfblup_prediction_all_9001_10000=readRDS(file="H2_1_gfblup_prediction_all_9001_10000.rds")
+H2_1_gfblup_prediction_all_10001_11000=readRDS(file="H2_1_gfblup_prediction_all_10001_11000.rds")
+H2_1_gfblup_prediction_all_11001_12419=readRDS(file="H2_1_gfblup_prediction_all_11001_12419.rds")
+
+H2_1_gfblup_variances_all_1_1000=readRDS(file="H2_1_gfblup_variances_all_1_1000.rds")
+H2_1_gfblup_variances_all_1001_2000=readRDS(file="H2_1_gfblup_variances_all_1001_2000.rds")
+H2_1_gfblup_variances_all_2001_3000=readRDS(file="H2_1_gfblup_variances_all_2001_3000.rds")
+H2_1_gfblup_variances_all_3001_4000=readRDS(file="H2_1_gfblup_variances_all_3001_4000.rds")
+H2_1_gfblup_variances_all_4001_5000=readRDS(file="H2_1_gfblup_variances_all_4001_5000.rds")
+H2_1_gfblup_variances_all_5001_6000=readRDS(file="H2_1_gfblup_variances_all_5001_6000.rds")
+H2_1_gfblup_variances_all_6001_7000=readRDS(file="H2_1_gfblup_variances_all_6001_7000.rds")
+H2_1_gfblup_variances_all_7001_8000=readRDS(file="H2_1_gfblup_variances_all_7001_8000.rds")
+H2_1_gfblup_variances_all_8001_9000=readRDS(file="H2_1_gfblup_variances_all_8001_9000.rds")
+H2_1_gfblup_variances_all_9001_10000=readRDS(file="H2_1_gfblup_variances_all_9001_10000.rds")
+H2_1_gfblup_variances_all_10001_11000=readRDS(file="H2_1_gfblup_variances_all_10001_11000.rds")
+H2_1_gfblup_variances_all_11001_12419=readRDS(file="H2_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H2_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H2_1_gfblup_variances_all=rep(list(list()),cycles)
+H2_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_1_1000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_1001_2000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_2001_3000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_3001_4000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_4001_5000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_5001_6000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_6001_7000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_7001_8000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_8001_9000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_9001_10000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_10001_11000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_11001_12419[[r]])
+
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_1_1000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_1001_2000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_2001_3000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_3001_4000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_4001_5000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_5001_6000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_6001_7000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_7001_8000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_8001_9000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_9001_10000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_10001_11000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H2_1_gfblup_prediction_all,"H2_1_gfblup_prediction_all.rds")
+saveRDS(H2_1_gfblup_variances_all,"H2_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H2_2_gblup_prediction_all_1_1000=readRDS(file="H2_2_gblup_prediction_all_1_1000.rds")
+H2_2_gblup_prediction_all_1001_2000=readRDS(file="H2_2_gblup_prediction_all_1001_2000.rds")
+H2_2_gblup_prediction_all_2001_3000=readRDS(file="H2_2_gblup_prediction_all_2001_3000.rds")
+H2_2_gblup_prediction_all_3001_4000=readRDS(file="H2_2_gblup_prediction_all_3001_4000.rds")
+H2_2_gblup_prediction_all_4001_5000=readRDS(file="H2_2_gblup_prediction_all_4001_5000.rds")
+H2_2_gblup_prediction_all_5001_6000=readRDS(file="H2_2_gblup_prediction_all_5001_6000.rds")
+H2_2_gblup_prediction_all_6001_7000=readRDS(file="H2_2_gblup_prediction_all_6001_7000.rds")
+H2_2_gblup_prediction_all_7001_8000=readRDS(file="H2_2_gblup_prediction_all_7001_8000.rds")
+H2_2_gblup_prediction_all_8001_9000=readRDS(file="H2_2_gblup_prediction_all_8001_9000.rds")
+H2_2_gblup_prediction_all_9001_10000=readRDS(file="H2_2_gblup_prediction_all_9001_10000.rds")
+H2_2_gblup_prediction_all_10001_11000=readRDS(file="H2_2_gblup_prediction_all_10001_11000.rds")
+H2_2_gblup_prediction_all_11001_12419=readRDS(file="H2_2_gblup_prediction_all_11001_12419.rds")
+H2_2_gblup_prediction_all=c(H2_2_gblup_prediction_all_1_1000,H2_2_gblup_prediction_all_1001_2000,H2_2_gblup_prediction_all_2001_3000,H2_2_gblup_prediction_all_3001_4000,H2_2_gblup_prediction_all_4001_5000,H2_2_gblup_prediction_all_5001_6000,H2_2_gblup_prediction_all_6001_7000,H2_2_gblup_prediction_all_7001_8000,H2_2_gblup_prediction_all_8001_9000,H2_2_gblup_prediction_all_9001_10000,H2_2_gblup_prediction_all_10001_11000,H2_2_gblup_prediction_all_11001_12419)
+
+H2_2_gblup_variances_all_1_1000=readRDS(file="H2_2_gblup_variances_all_1_1000.rds")
+H2_2_gblup_variances_all_1001_2000=readRDS(file="H2_2_gblup_variances_all_1001_2000.rds")
+H2_2_gblup_variances_all_2001_3000=readRDS(file="H2_2_gblup_variances_all_2001_3000.rds")
+H2_2_gblup_variances_all_3001_4000=readRDS(file="H2_2_gblup_variances_all_3001_4000.rds")
+H2_2_gblup_variances_all_4001_5000=readRDS(file="H2_2_gblup_variances_all_4001_5000.rds")
+H2_2_gblup_variances_all_5001_6000=readRDS(file="H2_2_gblup_variances_all_5001_6000.rds")
+H2_2_gblup_variances_all_6001_7000=readRDS(file="H2_2_gblup_variances_all_6001_7000.rds")
+H2_2_gblup_variances_all_7001_8000=readRDS(file="H2_2_gblup_variances_all_7001_8000.rds")
+H2_2_gblup_variances_all_8001_9000=readRDS(file="H2_2_gblup_variances_all_8001_9000.rds")
+H2_2_gblup_variances_all_9001_10000=readRDS(file="H2_2_gblup_variances_all_9001_10000.rds")
+H2_2_gblup_variances_all_10001_11000=readRDS(file="H2_2_gblup_variances_all_10001_11000.rds")
+H2_2_gblup_variances_all_11001_12419=readRDS(file="H2_2_gblup_variances_all_11001_12419.rds")
+H2_2_gblup_variances_all=c(H2_2_gblup_variances_all_1_1000,H2_2_gblup_variances_all_1001_2000,H2_2_gblup_variances_all_2001_3000,H2_2_gblup_variances_all_3001_4000,H2_2_gblup_variances_all_4001_5000,H2_2_gblup_variances_all_5001_6000,H2_2_gblup_variances_all_6001_7000,H2_2_gblup_variances_all_7001_8000,H2_2_gblup_variances_all_8001_9000,H2_2_gblup_variances_all_9001_10000,H2_2_gblup_variances_all_10001_11000,H2_2_gblup_variances_all_11001_12419)
+
+saveRDS(H2_2_gblup_prediction_all,"H2_2_gblup_prediction_all.rds")
+saveRDS(H2_2_gblup_variances_all,"H2_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H2_2_gfblup_prediction_all_1_1000=readRDS(file="H2_2_gfblup_prediction_all_1_1000.rds")
+H2_2_gfblup_prediction_all_1001_2000=readRDS(file="H2_2_gfblup_prediction_all_1001_2000.rds")
+H2_2_gfblup_prediction_all_2001_3000=readRDS(file="H2_2_gfblup_prediction_all_2001_3000.rds")
+H2_2_gfblup_prediction_all_3001_4000=readRDS(file="H2_2_gfblup_prediction_all_3001_4000.rds")
+H2_2_gfblup_prediction_all_4001_5000=readRDS(file="H2_2_gfblup_prediction_all_4001_5000.rds")
+H2_2_gfblup_prediction_all_5001_6000=readRDS(file="H2_2_gfblup_prediction_all_5001_6000.rds")
+H2_2_gfblup_prediction_all_6001_7000=readRDS(file="H2_2_gfblup_prediction_all_6001_7000.rds")
+H2_2_gfblup_prediction_all_7001_8000=readRDS(file="H2_2_gfblup_prediction_all_7001_8000.rds")
+H2_2_gfblup_prediction_all_8001_9000=readRDS(file="H2_2_gfblup_prediction_all_8001_9000.rds")
+H2_2_gfblup_prediction_all_9001_10000=readRDS(file="H2_2_gfblup_prediction_all_9001_10000.rds")
+H2_2_gfblup_prediction_all_10001_11000=readRDS(file="H2_2_gfblup_prediction_all_10001_11000.rds")
+H2_2_gfblup_prediction_all_11001_12419=readRDS(file="H2_2_gfblup_prediction_all_11001_12419.rds")
+
+H2_2_gfblup_variances_all_1_1000=readRDS(file="H2_2_gfblup_variances_all_1_1000.rds")
+H2_2_gfblup_variances_all_1001_2000=readRDS(file="H2_2_gfblup_variances_all_1001_2000.rds")
+H2_2_gfblup_variances_all_2001_3000=readRDS(file="H2_2_gfblup_variances_all_2001_3000.rds")
+H2_2_gfblup_variances_all_3001_4000=readRDS(file="H2_2_gfblup_variances_all_3001_4000.rds")
+H2_2_gfblup_variances_all_4001_5000=readRDS(file="H2_2_gfblup_variances_all_4001_5000.rds")
+H2_2_gfblup_variances_all_5001_6000=readRDS(file="H2_2_gfblup_variances_all_5001_6000.rds")
+H2_2_gfblup_variances_all_6001_7000=readRDS(file="H2_2_gfblup_variances_all_6001_7000.rds")
+H2_2_gfblup_variances_all_7001_8000=readRDS(file="H2_2_gfblup_variances_all_7001_8000.rds")
+H2_2_gfblup_variances_all_8001_9000=readRDS(file="H2_2_gfblup_variances_all_8001_9000.rds")
+H2_2_gfblup_variances_all_9001_10000=readRDS(file="H2_2_gfblup_variances_all_9001_10000.rds")
+H2_2_gfblup_variances_all_10001_11000=readRDS(file="H2_2_gfblup_variances_all_10001_11000.rds")
+H2_2_gfblup_variances_all_11001_12419=readRDS(file="H2_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H2_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H2_2_gfblup_variances_all=rep(list(list()),cycles)
+H2_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_1_1000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_1001_2000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_2001_3000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_3001_4000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_4001_5000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_5001_6000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_6001_7000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_7001_8000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_8001_9000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_9001_10000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_10001_11000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_11001_12419[[r]])
+
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_1_1000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_1001_2000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_2001_3000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_3001_4000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_4001_5000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_5001_6000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_6001_7000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_7001_8000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_8001_9000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_9001_10000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_10001_11000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H2_2_gfblup_prediction_all,"H2_2_gfblup_prediction_all.rds")
+saveRDS(H2_2_gfblup_variances_all,"H2_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H2_3_gblup_prediction_all_1_1000=readRDS(file="H2_3_gblup_prediction_all_1_1000.rds")
+H2_3_gblup_prediction_all_1001_2000=readRDS(file="H2_3_gblup_prediction_all_1001_2000.rds")
+H2_3_gblup_prediction_all_2001_3000=readRDS(file="H2_3_gblup_prediction_all_2001_3000.rds")
+H2_3_gblup_prediction_all_3001_4000=readRDS(file="H2_3_gblup_prediction_all_3001_4000.rds")
+H2_3_gblup_prediction_all_4001_5000=readRDS(file="H2_3_gblup_prediction_all_4001_5000.rds")
+H2_3_gblup_prediction_all_5001_6000=readRDS(file="H2_3_gblup_prediction_all_5001_6000.rds")
+H2_3_gblup_prediction_all_6001_7000=readRDS(file="H2_3_gblup_prediction_all_6001_7000.rds")
+H2_3_gblup_prediction_all_7001_8000=readRDS(file="H2_3_gblup_prediction_all_7001_8000.rds")
+H2_3_gblup_prediction_all_8001_9000=readRDS(file="H2_3_gblup_prediction_all_8001_9000.rds")
+H2_3_gblup_prediction_all_9001_10000=readRDS(file="H2_3_gblup_prediction_all_9001_10000.rds")
+H2_3_gblup_prediction_all_10001_11000=readRDS(file="H2_3_gblup_prediction_all_10001_11000.rds")
+H2_3_gblup_prediction_all_11001_12419=readRDS(file="H2_3_gblup_prediction_all_11001_12419.rds")
+H2_3_gblup_prediction_all=c(H2_3_gblup_prediction_all_1_1000,H2_3_gblup_prediction_all_1001_2000,H2_3_gblup_prediction_all_2001_3000,H2_3_gblup_prediction_all_3001_4000,H2_3_gblup_prediction_all_4001_5000,H2_3_gblup_prediction_all_5001_6000,H2_3_gblup_prediction_all_6001_7000,H2_3_gblup_prediction_all_7001_8000,H2_3_gblup_prediction_all_8001_9000,H2_3_gblup_prediction_all_9001_10000,H2_3_gblup_prediction_all_10001_11000,H2_3_gblup_prediction_all_11001_12419)
+
+H2_3_gblup_variances_all_1_1000=readRDS(file="H2_3_gblup_variances_all_1_1000.rds")
+H2_3_gblup_variances_all_1001_2000=readRDS(file="H2_3_gblup_variances_all_1001_2000.rds")
+H2_3_gblup_variances_all_2001_3000=readRDS(file="H2_3_gblup_variances_all_2001_3000.rds")
+H2_3_gblup_variances_all_3001_4000=readRDS(file="H2_3_gblup_variances_all_3001_4000.rds")
+H2_3_gblup_variances_all_4001_5000=readRDS(file="H2_3_gblup_variances_all_4001_5000.rds")
+H2_3_gblup_variances_all_5001_6000=readRDS(file="H2_3_gblup_variances_all_5001_6000.rds")
+H2_3_gblup_variances_all_6001_7000=readRDS(file="H2_3_gblup_variances_all_6001_7000.rds")
+H2_3_gblup_variances_all_7001_8000=readRDS(file="H2_3_gblup_variances_all_7001_8000.rds")
+H2_3_gblup_variances_all_8001_9000=readRDS(file="H2_3_gblup_variances_all_8001_9000.rds")
+H2_3_gblup_variances_all_9001_10000=readRDS(file="H2_3_gblup_variances_all_9001_10000.rds")
+H2_3_gblup_variances_all_10001_11000=readRDS(file="H2_3_gblup_variances_all_10001_11000.rds")
+H2_3_gblup_variances_all_11001_12419=readRDS(file="H2_3_gblup_variances_all_11001_12419.rds")
+H2_3_gblup_variances_all=c(H2_3_gblup_variances_all_1_1000,H2_3_gblup_variances_all_1001_2000,H2_3_gblup_variances_all_2001_3000,H2_3_gblup_variances_all_3001_4000,H2_3_gblup_variances_all_4001_5000,H2_3_gblup_variances_all_5001_6000,H2_3_gblup_variances_all_6001_7000,H2_3_gblup_variances_all_7001_8000,H2_3_gblup_variances_all_8001_9000,H2_3_gblup_variances_all_9001_10000,H2_3_gblup_variances_all_10001_11000,H2_3_gblup_variances_all_11001_12419)
+
+saveRDS(H2_3_gblup_prediction_all,"H2_3_gblup_prediction_all.rds")
+saveRDS(H2_3_gblup_variances_all,"H2_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H2_3_gfblup_prediction_all_1_1000=readRDS(file="H2_3_gfblup_prediction_all_1_1000.rds")
+H2_3_gfblup_prediction_all_1001_2000=readRDS(file="H2_3_gfblup_prediction_all_1001_2000.rds")
+H2_3_gfblup_prediction_all_2001_3000=readRDS(file="H2_3_gfblup_prediction_all_2001_3000.rds")
+H2_3_gfblup_prediction_all_3001_4000=readRDS(file="H2_3_gfblup_prediction_all_3001_4000.rds")
+H2_3_gfblup_prediction_all_4001_5000=readRDS(file="H2_3_gfblup_prediction_all_4001_5000.rds")
+H2_3_gfblup_prediction_all_5001_6000=readRDS(file="H2_3_gfblup_prediction_all_5001_6000.rds")
+H2_3_gfblup_prediction_all_6001_7000=readRDS(file="H2_3_gfblup_prediction_all_6001_7000.rds")
+H2_3_gfblup_prediction_all_7001_8000=readRDS(file="H2_3_gfblup_prediction_all_7001_8000.rds")
+H2_3_gfblup_prediction_all_8001_9000=readRDS(file="H2_3_gfblup_prediction_all_8001_9000.rds")
+H2_3_gfblup_prediction_all_9001_10000=readRDS(file="H2_3_gfblup_prediction_all_9001_10000.rds")
+H2_3_gfblup_prediction_all_10001_11000=readRDS(file="H2_3_gfblup_prediction_all_10001_11000.rds")
+H2_3_gfblup_prediction_all_11001_12419=readRDS(file="H2_3_gfblup_prediction_all_11001_12419.rds")
+
+H2_3_gfblup_variances_all_1_1000=readRDS(file="H2_3_gfblup_variances_all_1_1000.rds")
+H2_3_gfblup_variances_all_1001_2000=readRDS(file="H2_3_gfblup_variances_all_1001_2000.rds")
+H2_3_gfblup_variances_all_2001_3000=readRDS(file="H2_3_gfblup_variances_all_2001_3000.rds")
+H2_3_gfblup_variances_all_3001_4000=readRDS(file="H2_3_gfblup_variances_all_3001_4000.rds")
+H2_3_gfblup_variances_all_4001_5000=readRDS(file="H2_3_gfblup_variances_all_4001_5000.rds")
+H2_3_gfblup_variances_all_5001_6000=readRDS(file="H2_3_gfblup_variances_all_5001_6000.rds")
+H2_3_gfblup_variances_all_6001_7000=readRDS(file="H2_3_gfblup_variances_all_6001_7000.rds")
+H2_3_gfblup_variances_all_7001_8000=readRDS(file="H2_3_gfblup_variances_all_7001_8000.rds")
+H2_3_gfblup_variances_all_8001_9000=readRDS(file="H2_3_gfblup_variances_all_8001_9000.rds")
+H2_3_gfblup_variances_all_9001_10000=readRDS(file="H2_3_gfblup_variances_all_9001_10000.rds")
+H2_3_gfblup_variances_all_10001_11000=readRDS(file="H2_3_gfblup_variances_all_10001_11000.rds")
+H2_3_gfblup_variances_all_11001_12419=readRDS(file="H2_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H2_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H2_3_gfblup_variances_all=rep(list(list()),cycles)
+H2_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_1_1000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_1001_2000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_2001_3000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_3001_4000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_4001_5000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_5001_6000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_6001_7000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_7001_8000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_8001_9000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_9001_10000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_10001_11000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_11001_12419[[r]])
+
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_1_1000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_1001_2000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_2001_3000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_3001_4000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_4001_5000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_5001_6000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_6001_7000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_7001_8000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_8001_9000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_9001_10000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_10001_11000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H2_3_gfblup_prediction_all,"H2_3_gfblup_prediction_all.rds")
+saveRDS(H2_3_gfblup_variances_all,"H2_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H3_1_gblup_prediction_all_1_1000=readRDS(file="H3_1_gblup_prediction_all_1_1000.rds")
+H3_1_gblup_prediction_all_1001_2000=readRDS(file="H3_1_gblup_prediction_all_1001_2000.rds")
+H3_1_gblup_prediction_all_2001_3000=readRDS(file="H3_1_gblup_prediction_all_2001_3000.rds")
+H3_1_gblup_prediction_all_3001_4000=readRDS(file="H3_1_gblup_prediction_all_3001_4000.rds")
+H3_1_gblup_prediction_all_4001_5000=readRDS(file="H3_1_gblup_prediction_all_4001_5000.rds")
+H3_1_gblup_prediction_all_5001_6000=readRDS(file="H3_1_gblup_prediction_all_5001_6000.rds")
+H3_1_gblup_prediction_all_6001_7000=readRDS(file="H3_1_gblup_prediction_all_6001_7000.rds")
+H3_1_gblup_prediction_all_7001_8000=readRDS(file="H3_1_gblup_prediction_all_7001_8000.rds")
+H3_1_gblup_prediction_all_8001_9000=readRDS(file="H3_1_gblup_prediction_all_8001_9000.rds")
+H3_1_gblup_prediction_all_9001_10000=readRDS(file="H3_1_gblup_prediction_all_9001_10000.rds")
+H3_1_gblup_prediction_all_10001_11000=readRDS(file="H3_1_gblup_prediction_all_10001_11000.rds")
+H3_1_gblup_prediction_all_11001_12419=readRDS(file="H3_1_gblup_prediction_all_11001_12419.rds")
+H3_1_gblup_prediction_all=c(H3_1_gblup_prediction_all_1_1000,H3_1_gblup_prediction_all_1001_2000,H3_1_gblup_prediction_all_2001_3000,H3_1_gblup_prediction_all_3001_4000,H3_1_gblup_prediction_all_4001_5000,H3_1_gblup_prediction_all_5001_6000,H3_1_gblup_prediction_all_6001_7000,H3_1_gblup_prediction_all_7001_8000,H3_1_gblup_prediction_all_8001_9000,H3_1_gblup_prediction_all_9001_10000,H3_1_gblup_prediction_all_10001_11000,H3_1_gblup_prediction_all_11001_12419)
+
+H3_1_gblup_variances_all_1_1000=readRDS(file="H3_1_gblup_variances_all_1_1000.rds")
+H3_1_gblup_variances_all_1001_2000=readRDS(file="H3_1_gblup_variances_all_1001_2000.rds")
+H3_1_gblup_variances_all_2001_3000=readRDS(file="H3_1_gblup_variances_all_2001_3000.rds")
+H3_1_gblup_variances_all_3001_4000=readRDS(file="H3_1_gblup_variances_all_3001_4000.rds")
+H3_1_gblup_variances_all_4001_5000=readRDS(file="H3_1_gblup_variances_all_4001_5000.rds")
+H3_1_gblup_variances_all_5001_6000=readRDS(file="H3_1_gblup_variances_all_5001_6000.rds")
+H3_1_gblup_variances_all_6001_7000=readRDS(file="H3_1_gblup_variances_all_6001_7000.rds")
+H3_1_gblup_variances_all_7001_8000=readRDS(file="H3_1_gblup_variances_all_7001_8000.rds")
+H3_1_gblup_variances_all_8001_9000=readRDS(file="H3_1_gblup_variances_all_8001_9000.rds")
+H3_1_gblup_variances_all_9001_10000=readRDS(file="H3_1_gblup_variances_all_9001_10000.rds")
+H3_1_gblup_variances_all_10001_11000=readRDS(file="H3_1_gblup_variances_all_10001_11000.rds")
+H3_1_gblup_variances_all_11001_12419=readRDS(file="H3_1_gblup_variances_all_11001_12419.rds")
+H3_1_gblup_variances_all=c(H3_1_gblup_variances_all_1_1000,H3_1_gblup_variances_all_1001_2000,H3_1_gblup_variances_all_2001_3000,H3_1_gblup_variances_all_3001_4000,H3_1_gblup_variances_all_4001_5000,H3_1_gblup_variances_all_5001_6000,H3_1_gblup_variances_all_6001_7000,H3_1_gblup_variances_all_7001_8000,H3_1_gblup_variances_all_8001_9000,H3_1_gblup_variances_all_9001_10000,H3_1_gblup_variances_all_10001_11000,H3_1_gblup_variances_all_11001_12419)
+
+saveRDS(H3_1_gblup_prediction_all,"H3_1_gblup_prediction_all.rds")
+saveRDS(H3_1_gblup_variances_all,"H3_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H3_1_gfblup_prediction_all_1_1000=readRDS(file="H3_1_gfblup_prediction_all_1_1000.rds")
+H3_1_gfblup_prediction_all_1001_2000=readRDS(file="H3_1_gfblup_prediction_all_1001_2000.rds")
+H3_1_gfblup_prediction_all_2001_3000=readRDS(file="H3_1_gfblup_prediction_all_2001_3000.rds")
+H3_1_gfblup_prediction_all_3001_4000=readRDS(file="H3_1_gfblup_prediction_all_3001_4000.rds")
+H3_1_gfblup_prediction_all_4001_5000=readRDS(file="H3_1_gfblup_prediction_all_4001_5000.rds")
+H3_1_gfblup_prediction_all_5001_6000=readRDS(file="H3_1_gfblup_prediction_all_5001_6000.rds")
+H3_1_gfblup_prediction_all_6001_7000=readRDS(file="H3_1_gfblup_prediction_all_6001_7000.rds")
+H3_1_gfblup_prediction_all_7001_8000=readRDS(file="H3_1_gfblup_prediction_all_7001_8000.rds")
+H3_1_gfblup_prediction_all_8001_9000=readRDS(file="H3_1_gfblup_prediction_all_8001_9000.rds")
+H3_1_gfblup_prediction_all_9001_10000=readRDS(file="H3_1_gfblup_prediction_all_9001_10000.rds")
+H3_1_gfblup_prediction_all_10001_11000=readRDS(file="H3_1_gfblup_prediction_all_10001_11000.rds")
+H3_1_gfblup_prediction_all_11001_12419=readRDS(file="H3_1_gfblup_prediction_all_11001_12419.rds")
+
+H3_1_gfblup_variances_all_1_1000=readRDS(file="H3_1_gfblup_variances_all_1_1000.rds")
+H3_1_gfblup_variances_all_1001_2000=readRDS(file="H3_1_gfblup_variances_all_1001_2000.rds")
+H3_1_gfblup_variances_all_2001_3000=readRDS(file="H3_1_gfblup_variances_all_2001_3000.rds")
+H3_1_gfblup_variances_all_3001_4000=readRDS(file="H3_1_gfblup_variances_all_3001_4000.rds")
+H3_1_gfblup_variances_all_4001_5000=readRDS(file="H3_1_gfblup_variances_all_4001_5000.rds")
+H3_1_gfblup_variances_all_5001_6000=readRDS(file="H3_1_gfblup_variances_all_5001_6000.rds")
+H3_1_gfblup_variances_all_6001_7000=readRDS(file="H3_1_gfblup_variances_all_6001_7000.rds")
+H3_1_gfblup_variances_all_7001_8000=readRDS(file="H3_1_gfblup_variances_all_7001_8000.rds")
+H3_1_gfblup_variances_all_8001_9000=readRDS(file="H3_1_gfblup_variances_all_8001_9000.rds")
+H3_1_gfblup_variances_all_9001_10000=readRDS(file="H3_1_gfblup_variances_all_9001_10000.rds")
+H3_1_gfblup_variances_all_10001_11000=readRDS(file="H3_1_gfblup_variances_all_10001_11000.rds")
+H3_1_gfblup_variances_all_11001_12419=readRDS(file="H3_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H3_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H3_1_gfblup_variances_all=rep(list(list()),cycles)
+H3_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_1_1000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_1001_2000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_2001_3000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_3001_4000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_4001_5000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_5001_6000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_6001_7000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_7001_8000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_8001_9000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_9001_10000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_10001_11000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_11001_12419[[r]])
+
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_1_1000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_1001_2000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_2001_3000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_3001_4000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_4001_5000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_5001_6000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_6001_7000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_7001_8000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_8001_9000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_9001_10000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_10001_11000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H3_1_gfblup_prediction_all,"H3_1_gfblup_prediction_all.rds")
+saveRDS(H3_1_gfblup_variances_all,"H3_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H3_2_gblup_prediction_all_1_1000=readRDS(file="H3_2_gblup_prediction_all_1_1000.rds")
+H3_2_gblup_prediction_all_1001_2000=readRDS(file="H3_2_gblup_prediction_all_1001_2000.rds")
+H3_2_gblup_prediction_all_2001_3000=readRDS(file="H3_2_gblup_prediction_all_2001_3000.rds")
+H3_2_gblup_prediction_all_3001_4000=readRDS(file="H3_2_gblup_prediction_all_3001_4000.rds")
+H3_2_gblup_prediction_all_4001_5000=readRDS(file="H3_2_gblup_prediction_all_4001_5000.rds")
+H3_2_gblup_prediction_all_5001_6000=readRDS(file="H3_2_gblup_prediction_all_5001_6000.rds")
+H3_2_gblup_prediction_all_6001_7000=readRDS(file="H3_2_gblup_prediction_all_6001_7000.rds")
+H3_2_gblup_prediction_all_7001_8000=readRDS(file="H3_2_gblup_prediction_all_7001_8000.rds")
+H3_2_gblup_prediction_all_8001_9000=readRDS(file="H3_2_gblup_prediction_all_8001_9000.rds")
+H3_2_gblup_prediction_all_9001_10000=readRDS(file="H3_2_gblup_prediction_all_9001_10000.rds")
+H3_2_gblup_prediction_all_10001_11000=readRDS(file="H3_2_gblup_prediction_all_10001_11000.rds")
+H3_2_gblup_prediction_all_11001_12419=readRDS(file="H3_2_gblup_prediction_all_11001_12419.rds")
+H3_2_gblup_prediction_all=c(H3_2_gblup_prediction_all_1_1000,H3_2_gblup_prediction_all_1001_2000,H3_2_gblup_prediction_all_2001_3000,H3_2_gblup_prediction_all_3001_4000,H3_2_gblup_prediction_all_4001_5000,H3_2_gblup_prediction_all_5001_6000,H3_2_gblup_prediction_all_6001_7000,H3_2_gblup_prediction_all_7001_8000,H3_2_gblup_prediction_all_8001_9000,H3_2_gblup_prediction_all_9001_10000,H3_2_gblup_prediction_all_10001_11000,H3_2_gblup_prediction_all_11001_12419)
+
+H3_2_gblup_variances_all_1_1000=readRDS(file="H3_2_gblup_variances_all_1_1000.rds")
+H3_2_gblup_variances_all_1001_2000=readRDS(file="H3_2_gblup_variances_all_1001_2000.rds")
+H3_2_gblup_variances_all_2001_3000=readRDS(file="H3_2_gblup_variances_all_2001_3000.rds")
+H3_2_gblup_variances_all_3001_4000=readRDS(file="H3_2_gblup_variances_all_3001_4000.rds")
+H3_2_gblup_variances_all_4001_5000=readRDS(file="H3_2_gblup_variances_all_4001_5000.rds")
+H3_2_gblup_variances_all_5001_6000=readRDS(file="H3_2_gblup_variances_all_5001_6000.rds")
+H3_2_gblup_variances_all_6001_7000=readRDS(file="H3_2_gblup_variances_all_6001_7000.rds")
+H3_2_gblup_variances_all_7001_8000=readRDS(file="H3_2_gblup_variances_all_7001_8000.rds")
+H3_2_gblup_variances_all_8001_9000=readRDS(file="H3_2_gblup_variances_all_8001_9000.rds")
+H3_2_gblup_variances_all_9001_10000=readRDS(file="H3_2_gblup_variances_all_9001_10000.rds")
+H3_2_gblup_variances_all_10001_11000=readRDS(file="H3_2_gblup_variances_all_10001_11000.rds")
+H3_2_gblup_variances_all_11001_12419=readRDS(file="H3_2_gblup_variances_all_11001_12419.rds")
+H3_2_gblup_variances_all=c(H3_2_gblup_variances_all_1_1000,H3_2_gblup_variances_all_1001_2000,H3_2_gblup_variances_all_2001_3000,H3_2_gblup_variances_all_3001_4000,H3_2_gblup_variances_all_4001_5000,H3_2_gblup_variances_all_5001_6000,H3_2_gblup_variances_all_6001_7000,H3_2_gblup_variances_all_7001_8000,H3_2_gblup_variances_all_8001_9000,H3_2_gblup_variances_all_9001_10000,H3_2_gblup_variances_all_10001_11000,H3_2_gblup_variances_all_11001_12419)
+
+saveRDS(H3_2_gblup_prediction_all,"H3_2_gblup_prediction_all.rds")
+saveRDS(H3_2_gblup_variances_all,"H3_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H3_2_gfblup_prediction_all_1_1000=readRDS(file="H3_2_gfblup_prediction_all_1_1000.rds")
+H3_2_gfblup_prediction_all_1001_2000=readRDS(file="H3_2_gfblup_prediction_all_1001_2000.rds")
+H3_2_gfblup_prediction_all_2001_3000=readRDS(file="H3_2_gfblup_prediction_all_2001_3000.rds")
+H3_2_gfblup_prediction_all_3001_4000=readRDS(file="H3_2_gfblup_prediction_all_3001_4000.rds")
+H3_2_gfblup_prediction_all_4001_5000=readRDS(file="H3_2_gfblup_prediction_all_4001_5000.rds")
+H3_2_gfblup_prediction_all_5001_6000=readRDS(file="H3_2_gfblup_prediction_all_5001_6000.rds")
+H3_2_gfblup_prediction_all_6001_7000=readRDS(file="H3_2_gfblup_prediction_all_6001_7000.rds")
+H3_2_gfblup_prediction_all_7001_8000=readRDS(file="H3_2_gfblup_prediction_all_7001_8000.rds")
+H3_2_gfblup_prediction_all_8001_9000=readRDS(file="H3_2_gfblup_prediction_all_8001_9000.rds")
+H3_2_gfblup_prediction_all_9001_10000=readRDS(file="H3_2_gfblup_prediction_all_9001_10000.rds")
+H3_2_gfblup_prediction_all_10001_11000=readRDS(file="H3_2_gfblup_prediction_all_10001_11000.rds")
+H3_2_gfblup_prediction_all_11001_12419=readRDS(file="H3_2_gfblup_prediction_all_11001_12419.rds")
+
+H3_2_gfblup_variances_all_1_1000=readRDS(file="H3_2_gfblup_variances_all_1_1000.rds")
+H3_2_gfblup_variances_all_1001_2000=readRDS(file="H3_2_gfblup_variances_all_1001_2000.rds")
+H3_2_gfblup_variances_all_2001_3000=readRDS(file="H3_2_gfblup_variances_all_2001_3000.rds")
+H3_2_gfblup_variances_all_3001_4000=readRDS(file="H3_2_gfblup_variances_all_3001_4000.rds")
+H3_2_gfblup_variances_all_4001_5000=readRDS(file="H3_2_gfblup_variances_all_4001_5000.rds")
+H3_2_gfblup_variances_all_5001_6000=readRDS(file="H3_2_gfblup_variances_all_5001_6000.rds")
+H3_2_gfblup_variances_all_6001_7000=readRDS(file="H3_2_gfblup_variances_all_6001_7000.rds")
+H3_2_gfblup_variances_all_7001_8000=readRDS(file="H3_2_gfblup_variances_all_7001_8000.rds")
+H3_2_gfblup_variances_all_8001_9000=readRDS(file="H3_2_gfblup_variances_all_8001_9000.rds")
+H3_2_gfblup_variances_all_9001_10000=readRDS(file="H3_2_gfblup_variances_all_9001_10000.rds")
+H3_2_gfblup_variances_all_10001_11000=readRDS(file="H3_2_gfblup_variances_all_10001_11000.rds")
+H3_2_gfblup_variances_all_11001_12419=readRDS(file="H3_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H3_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H3_2_gfblup_variances_all=rep(list(list()),cycles)
+H3_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_1_1000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_1001_2000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_2001_3000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_3001_4000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_4001_5000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_5001_6000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_6001_7000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_7001_8000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_8001_9000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_9001_10000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_10001_11000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_11001_12419[[r]])
+
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_1_1000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_1001_2000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_2001_3000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_3001_4000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_4001_5000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_5001_6000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_6001_7000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_7001_8000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_8001_9000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_9001_10000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_10001_11000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H3_2_gfblup_prediction_all,"H3_2_gfblup_prediction_all.rds")
+saveRDS(H3_2_gfblup_variances_all,"H3_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H3_3_gblup_prediction_all_1_1000=readRDS(file="H3_3_gblup_prediction_all_1_1000.rds")
+H3_3_gblup_prediction_all_1001_2000=readRDS(file="H3_3_gblup_prediction_all_1001_2000.rds")
+H3_3_gblup_prediction_all_2001_3000=readRDS(file="H3_3_gblup_prediction_all_2001_3000.rds")
+H3_3_gblup_prediction_all_3001_4000=readRDS(file="H3_3_gblup_prediction_all_3001_4000.rds")
+H3_3_gblup_prediction_all_4001_5000=readRDS(file="H3_3_gblup_prediction_all_4001_5000.rds")
+H3_3_gblup_prediction_all_5001_6000=readRDS(file="H3_3_gblup_prediction_all_5001_6000.rds")
+H3_3_gblup_prediction_all_6001_7000=readRDS(file="H3_3_gblup_prediction_all_6001_7000.rds")
+H3_3_gblup_prediction_all_7001_8000=readRDS(file="H3_3_gblup_prediction_all_7001_8000.rds")
+H3_3_gblup_prediction_all_8001_9000=readRDS(file="H3_3_gblup_prediction_all_8001_9000.rds")
+H3_3_gblup_prediction_all_9001_10000=readRDS(file="H3_3_gblup_prediction_all_9001_10000.rds")
+H3_3_gblup_prediction_all_10001_11000=readRDS(file="H3_3_gblup_prediction_all_10001_11000.rds")
+H3_3_gblup_prediction_all_11001_12419=readRDS(file="H3_3_gblup_prediction_all_11001_12419.rds")
+H3_3_gblup_prediction_all=c(H3_3_gblup_prediction_all_1_1000,H3_3_gblup_prediction_all_1001_2000,H3_3_gblup_prediction_all_2001_3000,H3_3_gblup_prediction_all_3001_4000,H3_3_gblup_prediction_all_4001_5000,H3_3_gblup_prediction_all_5001_6000,H3_3_gblup_prediction_all_6001_7000,H3_3_gblup_prediction_all_7001_8000,H3_3_gblup_prediction_all_8001_9000,H3_3_gblup_prediction_all_9001_10000,H3_3_gblup_prediction_all_10001_11000,H3_3_gblup_prediction_all_11001_12419)
+
+H3_3_gblup_variances_all_1_1000=readRDS(file="H3_3_gblup_variances_all_1_1000.rds")
+H3_3_gblup_variances_all_1001_2000=readRDS(file="H3_3_gblup_variances_all_1001_2000.rds")
+H3_3_gblup_variances_all_2001_3000=readRDS(file="H3_3_gblup_variances_all_2001_3000.rds")
+H3_3_gblup_variances_all_3001_4000=readRDS(file="H3_3_gblup_variances_all_3001_4000.rds")
+H3_3_gblup_variances_all_4001_5000=readRDS(file="H3_3_gblup_variances_all_4001_5000.rds")
+H3_3_gblup_variances_all_5001_6000=readRDS(file="H3_3_gblup_variances_all_5001_6000.rds")
+H3_3_gblup_variances_all_6001_7000=readRDS(file="H3_3_gblup_variances_all_6001_7000.rds")
+H3_3_gblup_variances_all_7001_8000=readRDS(file="H3_3_gblup_variances_all_7001_8000.rds")
+H3_3_gblup_variances_all_8001_9000=readRDS(file="H3_3_gblup_variances_all_8001_9000.rds")
+H3_3_gblup_variances_all_9001_10000=readRDS(file="H3_3_gblup_variances_all_9001_10000.rds")
+H3_3_gblup_variances_all_10001_11000=readRDS(file="H3_3_gblup_variances_all_10001_11000.rds")
+H3_3_gblup_variances_all_11001_12419=readRDS(file="H3_3_gblup_variances_all_11001_12419.rds")
+H3_3_gblup_variances_all=c(H3_3_gblup_variances_all_1_1000,H3_3_gblup_variances_all_1001_2000,H3_3_gblup_variances_all_2001_3000,H3_3_gblup_variances_all_3001_4000,H3_3_gblup_variances_all_4001_5000,H3_3_gblup_variances_all_5001_6000,H3_3_gblup_variances_all_6001_7000,H3_3_gblup_variances_all_7001_8000,H3_3_gblup_variances_all_8001_9000,H3_3_gblup_variances_all_9001_10000,H3_3_gblup_variances_all_10001_11000,H3_3_gblup_variances_all_11001_12419)
+
+saveRDS(H3_3_gblup_prediction_all,"H3_3_gblup_prediction_all.rds")
+saveRDS(H3_3_gblup_variances_all,"H3_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H3_3_gfblup_prediction_all_1_1000=readRDS(file="H3_3_gfblup_prediction_all_1_1000.rds")
+H3_3_gfblup_prediction_all_1001_2000=readRDS(file="H3_3_gfblup_prediction_all_1001_2000.rds")
+H3_3_gfblup_prediction_all_2001_3000=readRDS(file="H3_3_gfblup_prediction_all_2001_3000.rds")
+H3_3_gfblup_prediction_all_3001_4000=readRDS(file="H3_3_gfblup_prediction_all_3001_4000.rds")
+H3_3_gfblup_prediction_all_4001_5000=readRDS(file="H3_3_gfblup_prediction_all_4001_5000.rds")
+H3_3_gfblup_prediction_all_5001_6000=readRDS(file="H3_3_gfblup_prediction_all_5001_6000.rds")
+H3_3_gfblup_prediction_all_6001_7000=readRDS(file="H3_3_gfblup_prediction_all_6001_7000.rds")
+H3_3_gfblup_prediction_all_7001_8000=readRDS(file="H3_3_gfblup_prediction_all_7001_8000.rds")
+H3_3_gfblup_prediction_all_8001_9000=readRDS(file="H3_3_gfblup_prediction_all_8001_9000.rds")
+H3_3_gfblup_prediction_all_9001_10000=readRDS(file="H3_3_gfblup_prediction_all_9001_10000.rds")
+H3_3_gfblup_prediction_all_10001_11000=readRDS(file="H3_3_gfblup_prediction_all_10001_11000.rds")
+H3_3_gfblup_prediction_all_11001_12419=readRDS(file="H3_3_gfblup_prediction_all_11001_12419.rds")
+
+H3_3_gfblup_variances_all_1_1000=readRDS(file="H3_3_gfblup_variances_all_1_1000.rds")
+H3_3_gfblup_variances_all_1001_2000=readRDS(file="H3_3_gfblup_variances_all_1001_2000.rds")
+H3_3_gfblup_variances_all_2001_3000=readRDS(file="H3_3_gfblup_variances_all_2001_3000.rds")
+H3_3_gfblup_variances_all_3001_4000=readRDS(file="H3_3_gfblup_variances_all_3001_4000.rds")
+H3_3_gfblup_variances_all_4001_5000=readRDS(file="H3_3_gfblup_variances_all_4001_5000.rds")
+H3_3_gfblup_variances_all_5001_6000=readRDS(file="H3_3_gfblup_variances_all_5001_6000.rds")
+H3_3_gfblup_variances_all_6001_7000=readRDS(file="H3_3_gfblup_variances_all_6001_7000.rds")
+H3_3_gfblup_variances_all_7001_8000=readRDS(file="H3_3_gfblup_variances_all_7001_8000.rds")
+H3_3_gfblup_variances_all_8001_9000=readRDS(file="H3_3_gfblup_variances_all_8001_9000.rds")
+H3_3_gfblup_variances_all_9001_10000=readRDS(file="H3_3_gfblup_variances_all_9001_10000.rds")
+H3_3_gfblup_variances_all_10001_11000=readRDS(file="H3_3_gfblup_variances_all_10001_11000.rds")
+H3_3_gfblup_variances_all_11001_12419=readRDS(file="H3_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H3_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H3_3_gfblup_variances_all=rep(list(list()),cycles)
+H3_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_1_1000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_1001_2000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_2001_3000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_3001_4000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_4001_5000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_5001_6000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_6001_7000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_7001_8000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_8001_9000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_9001_10000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_10001_11000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_11001_12419[[r]])
+
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_1_1000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_1001_2000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_2001_3000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_3001_4000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_4001_5000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_5001_6000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_6001_7000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_7001_8000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_8001_9000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_9001_10000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_10001_11000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H3_3_gfblup_prediction_all,"H3_3_gfblup_prediction_all.rds")
+saveRDS(H3_3_gfblup_variances_all,"H3_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H4_1_gblup_prediction_all_1_1000=readRDS(file="H4_1_gblup_prediction_all_1_1000.rds")
+H4_1_gblup_prediction_all_1001_2000=readRDS(file="H4_1_gblup_prediction_all_1001_2000.rds")
+H4_1_gblup_prediction_all_2001_3000=readRDS(file="H4_1_gblup_prediction_all_2001_3000.rds")
+H4_1_gblup_prediction_all_3001_4000=readRDS(file="H4_1_gblup_prediction_all_3001_4000.rds")
+H4_1_gblup_prediction_all_4001_5000=readRDS(file="H4_1_gblup_prediction_all_4001_5000.rds")
+H4_1_gblup_prediction_all_5001_6000=readRDS(file="H4_1_gblup_prediction_all_5001_6000.rds")
+H4_1_gblup_prediction_all_6001_7000=readRDS(file="H4_1_gblup_prediction_all_6001_7000.rds")
+H4_1_gblup_prediction_all_7001_8000=readRDS(file="H4_1_gblup_prediction_all_7001_8000.rds")
+H4_1_gblup_prediction_all_8001_9000=readRDS(file="H4_1_gblup_prediction_all_8001_9000.rds")
+H4_1_gblup_prediction_all_9001_10000=readRDS(file="H4_1_gblup_prediction_all_9001_10000.rds")
+H4_1_gblup_prediction_all_10001_11000=readRDS(file="H4_1_gblup_prediction_all_10001_11000.rds")
+H4_1_gblup_prediction_all_11001_12419=readRDS(file="H4_1_gblup_prediction_all_11001_12419.rds")
+H4_1_gblup_prediction_all=c(H4_1_gblup_prediction_all_1_1000,H4_1_gblup_prediction_all_1001_2000,H4_1_gblup_prediction_all_2001_3000,H4_1_gblup_prediction_all_3001_4000,H4_1_gblup_prediction_all_4001_5000,H4_1_gblup_prediction_all_5001_6000,H4_1_gblup_prediction_all_6001_7000,H4_1_gblup_prediction_all_7001_8000,H4_1_gblup_prediction_all_8001_9000,H4_1_gblup_prediction_all_9001_10000,H4_1_gblup_prediction_all_10001_11000,H4_1_gblup_prediction_all_11001_12419)
+
+H4_1_gblup_variances_all_1_1000=readRDS(file="H4_1_gblup_variances_all_1_1000.rds")
+H4_1_gblup_variances_all_1001_2000=readRDS(file="H4_1_gblup_variances_all_1001_2000.rds")
+H4_1_gblup_variances_all_2001_3000=readRDS(file="H4_1_gblup_variances_all_2001_3000.rds")
+H4_1_gblup_variances_all_3001_4000=readRDS(file="H4_1_gblup_variances_all_3001_4000.rds")
+H4_1_gblup_variances_all_4001_5000=readRDS(file="H4_1_gblup_variances_all_4001_5000.rds")
+H4_1_gblup_variances_all_5001_6000=readRDS(file="H4_1_gblup_variances_all_5001_6000.rds")
+H4_1_gblup_variances_all_6001_7000=readRDS(file="H4_1_gblup_variances_all_6001_7000.rds")
+H4_1_gblup_variances_all_7001_8000=readRDS(file="H4_1_gblup_variances_all_7001_8000.rds")
+H4_1_gblup_variances_all_8001_9000=readRDS(file="H4_1_gblup_variances_all_8001_9000.rds")
+H4_1_gblup_variances_all_9001_10000=readRDS(file="H4_1_gblup_variances_all_9001_10000.rds")
+H4_1_gblup_variances_all_10001_11000=readRDS(file="H4_1_gblup_variances_all_10001_11000.rds")
+H4_1_gblup_variances_all_11001_12419=readRDS(file="H4_1_gblup_variances_all_11001_12419.rds")
+H4_1_gblup_variances_all=c(H4_1_gblup_variances_all_1_1000,H4_1_gblup_variances_all_1001_2000,H4_1_gblup_variances_all_2001_3000,H4_1_gblup_variances_all_3001_4000,H4_1_gblup_variances_all_4001_5000,H4_1_gblup_variances_all_5001_6000,H4_1_gblup_variances_all_6001_7000,H4_1_gblup_variances_all_7001_8000,H4_1_gblup_variances_all_8001_9000,H4_1_gblup_variances_all_9001_10000,H4_1_gblup_variances_all_10001_11000,H4_1_gblup_variances_all_11001_12419)
+
+saveRDS(H4_1_gblup_prediction_all,"H4_1_gblup_prediction_all.rds")
+saveRDS(H4_1_gblup_variances_all,"H4_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H4_1_gfblup_prediction_all_1_1000=readRDS(file="H4_1_gfblup_prediction_all_1_1000.rds")
+H4_1_gfblup_prediction_all_1001_2000=readRDS(file="H4_1_gfblup_prediction_all_1001_2000.rds")
+H4_1_gfblup_prediction_all_2001_3000=readRDS(file="H4_1_gfblup_prediction_all_2001_3000.rds")
+H4_1_gfblup_prediction_all_3001_4000=readRDS(file="H4_1_gfblup_prediction_all_3001_4000.rds")
+H4_1_gfblup_prediction_all_4001_5000=readRDS(file="H4_1_gfblup_prediction_all_4001_5000.rds")
+H4_1_gfblup_prediction_all_5001_6000=readRDS(file="H4_1_gfblup_prediction_all_5001_6000.rds")
+H4_1_gfblup_prediction_all_6001_7000=readRDS(file="H4_1_gfblup_prediction_all_6001_7000.rds")
+H4_1_gfblup_prediction_all_7001_8000=readRDS(file="H4_1_gfblup_prediction_all_7001_8000.rds")
+H4_1_gfblup_prediction_all_8001_9000=readRDS(file="H4_1_gfblup_prediction_all_8001_9000.rds")
+H4_1_gfblup_prediction_all_9001_10000=readRDS(file="H4_1_gfblup_prediction_all_9001_10000.rds")
+H4_1_gfblup_prediction_all_10001_11000=readRDS(file="H4_1_gfblup_prediction_all_10001_11000.rds")
+H4_1_gfblup_prediction_all_11001_12419=readRDS(file="H4_1_gfblup_prediction_all_11001_12419.rds")
+
+H4_1_gfblup_variances_all_1_1000=readRDS(file="H4_1_gfblup_variances_all_1_1000.rds")
+H4_1_gfblup_variances_all_1001_2000=readRDS(file="H4_1_gfblup_variances_all_1001_2000.rds")
+H4_1_gfblup_variances_all_2001_3000=readRDS(file="H4_1_gfblup_variances_all_2001_3000.rds")
+H4_1_gfblup_variances_all_3001_4000=readRDS(file="H4_1_gfblup_variances_all_3001_4000.rds")
+H4_1_gfblup_variances_all_4001_5000=readRDS(file="H4_1_gfblup_variances_all_4001_5000.rds")
+H4_1_gfblup_variances_all_5001_6000=readRDS(file="H4_1_gfblup_variances_all_5001_6000.rds")
+H4_1_gfblup_variances_all_6001_7000=readRDS(file="H4_1_gfblup_variances_all_6001_7000.rds")
+H4_1_gfblup_variances_all_7001_8000=readRDS(file="H4_1_gfblup_variances_all_7001_8000.rds")
+H4_1_gfblup_variances_all_8001_9000=readRDS(file="H4_1_gfblup_variances_all_8001_9000.rds")
+H4_1_gfblup_variances_all_9001_10000=readRDS(file="H4_1_gfblup_variances_all_9001_10000.rds")
+H4_1_gfblup_variances_all_10001_11000=readRDS(file="H4_1_gfblup_variances_all_10001_11000.rds")
+H4_1_gfblup_variances_all_11001_12419=readRDS(file="H4_1_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H4_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H4_1_gfblup_variances_all=rep(list(list()),cycles)
+H4_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_1_1000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_1001_2000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_2001_3000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_3001_4000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_4001_5000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_5001_6000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_6001_7000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_7001_8000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_8001_9000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_9001_10000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_10001_11000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_11001_12419[[r]])
+
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_1_1000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_1001_2000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_2001_3000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_3001_4000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_4001_5000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_5001_6000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_6001_7000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_7001_8000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_8001_9000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_9001_10000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_10001_11000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H4_1_gfblup_prediction_all,"H4_1_gfblup_prediction_all.rds")
+saveRDS(H4_1_gfblup_variances_all,"H4_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H4_2_gblup_prediction_all_1_1000=readRDS(file="H4_2_gblup_prediction_all_1_1000.rds")
+H4_2_gblup_prediction_all_1001_2000=readRDS(file="H4_2_gblup_prediction_all_1001_2000.rds")
+H4_2_gblup_prediction_all_2001_3000=readRDS(file="H4_2_gblup_prediction_all_2001_3000.rds")
+H4_2_gblup_prediction_all_3001_4000=readRDS(file="H4_2_gblup_prediction_all_3001_4000.rds")
+H4_2_gblup_prediction_all_4001_5000=readRDS(file="H4_2_gblup_prediction_all_4001_5000.rds")
+H4_2_gblup_prediction_all_5001_6000=readRDS(file="H4_2_gblup_prediction_all_5001_6000.rds")
+H4_2_gblup_prediction_all_6001_7000=readRDS(file="H4_2_gblup_prediction_all_6001_7000.rds")
+H4_2_gblup_prediction_all_7001_8000=readRDS(file="H4_2_gblup_prediction_all_7001_8000.rds")
+H4_2_gblup_prediction_all_8001_9000=readRDS(file="H4_2_gblup_prediction_all_8001_9000.rds")
+H4_2_gblup_prediction_all_9001_10000=readRDS(file="H4_2_gblup_prediction_all_9001_10000.rds")
+H4_2_gblup_prediction_all_10001_11000=readRDS(file="H4_2_gblup_prediction_all_10001_11000.rds")
+H4_2_gblup_prediction_all_11001_12419=readRDS(file="H4_2_gblup_prediction_all_11001_12419.rds")
+H4_2_gblup_prediction_all=c(H4_2_gblup_prediction_all_1_1000,H4_2_gblup_prediction_all_1001_2000,H4_2_gblup_prediction_all_2001_3000,H4_2_gblup_prediction_all_3001_4000,H4_2_gblup_prediction_all_4001_5000,H4_2_gblup_prediction_all_5001_6000,H4_2_gblup_prediction_all_6001_7000,H4_2_gblup_prediction_all_7001_8000,H4_2_gblup_prediction_all_8001_9000,H4_2_gblup_prediction_all_9001_10000,H4_2_gblup_prediction_all_10001_11000,H4_2_gblup_prediction_all_11001_12419)
+
+H4_2_gblup_variances_all_1_1000=readRDS(file="H4_2_gblup_variances_all_1_1000.rds")
+H4_2_gblup_variances_all_1001_2000=readRDS(file="H4_2_gblup_variances_all_1001_2000.rds")
+H4_2_gblup_variances_all_2001_3000=readRDS(file="H4_2_gblup_variances_all_2001_3000.rds")
+H4_2_gblup_variances_all_3001_4000=readRDS(file="H4_2_gblup_variances_all_3001_4000.rds")
+H4_2_gblup_variances_all_4001_5000=readRDS(file="H4_2_gblup_variances_all_4001_5000.rds")
+H4_2_gblup_variances_all_5001_6000=readRDS(file="H4_2_gblup_variances_all_5001_6000.rds")
+H4_2_gblup_variances_all_6001_7000=readRDS(file="H4_2_gblup_variances_all_6001_7000.rds")
+H4_2_gblup_variances_all_7001_8000=readRDS(file="H4_2_gblup_variances_all_7001_8000.rds")
+H4_2_gblup_variances_all_8001_9000=readRDS(file="H4_2_gblup_variances_all_8001_9000.rds")
+H4_2_gblup_variances_all_9001_10000=readRDS(file="H4_2_gblup_variances_all_9001_10000.rds")
+H4_2_gblup_variances_all_10001_11000=readRDS(file="H4_2_gblup_variances_all_10001_11000.rds")
+H4_2_gblup_variances_all_11001_12419=readRDS(file="H4_2_gblup_variances_all_11001_12419.rds")
+H4_2_gblup_variances_all=c(H4_2_gblup_variances_all_1_1000,H4_2_gblup_variances_all_1001_2000,H4_2_gblup_variances_all_2001_3000,H4_2_gblup_variances_all_3001_4000,H4_2_gblup_variances_all_4001_5000,H4_2_gblup_variances_all_5001_6000,H4_2_gblup_variances_all_6001_7000,H4_2_gblup_variances_all_7001_8000,H4_2_gblup_variances_all_8001_9000,H4_2_gblup_variances_all_9001_10000,H4_2_gblup_variances_all_10001_11000,H4_2_gblup_variances_all_11001_12419)
+
+saveRDS(H4_2_gblup_prediction_all,"H4_2_gblup_prediction_all.rds")
+saveRDS(H4_2_gblup_variances_all,"H4_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H4_2_gfblup_prediction_all_1_1000=readRDS(file="H4_2_gfblup_prediction_all_1_1000.rds")
+H4_2_gfblup_prediction_all_1001_2000=readRDS(file="H4_2_gfblup_prediction_all_1001_2000.rds")
+H4_2_gfblup_prediction_all_2001_3000=readRDS(file="H4_2_gfblup_prediction_all_2001_3000.rds")
+H4_2_gfblup_prediction_all_3001_4000=readRDS(file="H4_2_gfblup_prediction_all_3001_4000.rds")
+H4_2_gfblup_prediction_all_4001_5000=readRDS(file="H4_2_gfblup_prediction_all_4001_5000.rds")
+H4_2_gfblup_prediction_all_5001_6000=readRDS(file="H4_2_gfblup_prediction_all_5001_6000.rds")
+H4_2_gfblup_prediction_all_6001_7000=readRDS(file="H4_2_gfblup_prediction_all_6001_7000.rds")
+H4_2_gfblup_prediction_all_7001_8000=readRDS(file="H4_2_gfblup_prediction_all_7001_8000.rds")
+H4_2_gfblup_prediction_all_8001_9000=readRDS(file="H4_2_gfblup_prediction_all_8001_9000.rds")
+H4_2_gfblup_prediction_all_9001_10000=readRDS(file="H4_2_gfblup_prediction_all_9001_10000.rds")
+H4_2_gfblup_prediction_all_10001_11000=readRDS(file="H4_2_gfblup_prediction_all_10001_11000.rds")
+H4_2_gfblup_prediction_all_11001_12419=readRDS(file="H4_2_gfblup_prediction_all_11001_12419.rds")
+
+H4_2_gfblup_variances_all_1_1000=readRDS(file="H4_2_gfblup_variances_all_1_1000.rds")
+H4_2_gfblup_variances_all_1001_2000=readRDS(file="H4_2_gfblup_variances_all_1001_2000.rds")
+H4_2_gfblup_variances_all_2001_3000=readRDS(file="H4_2_gfblup_variances_all_2001_3000.rds")
+H4_2_gfblup_variances_all_3001_4000=readRDS(file="H4_2_gfblup_variances_all_3001_4000.rds")
+H4_2_gfblup_variances_all_4001_5000=readRDS(file="H4_2_gfblup_variances_all_4001_5000.rds")
+H4_2_gfblup_variances_all_5001_6000=readRDS(file="H4_2_gfblup_variances_all_5001_6000.rds")
+H4_2_gfblup_variances_all_6001_7000=readRDS(file="H4_2_gfblup_variances_all_6001_7000.rds")
+H4_2_gfblup_variances_all_7001_8000=readRDS(file="H4_2_gfblup_variances_all_7001_8000.rds")
+H4_2_gfblup_variances_all_8001_9000=readRDS(file="H4_2_gfblup_variances_all_8001_9000.rds")
+H4_2_gfblup_variances_all_9001_10000=readRDS(file="H4_2_gfblup_variances_all_9001_10000.rds")
+H4_2_gfblup_variances_all_10001_11000=readRDS(file="H4_2_gfblup_variances_all_10001_11000.rds")
+H4_2_gfblup_variances_all_11001_12419=readRDS(file="H4_2_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H4_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H4_2_gfblup_variances_all=rep(list(list()),cycles)
+H4_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_1_1000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_1001_2000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_2001_3000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_3001_4000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_4001_5000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_5001_6000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_6001_7000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_7001_8000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_8001_9000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_9001_10000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_10001_11000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_11001_12419[[r]])
+
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_1_1000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_1001_2000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_2001_3000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_3001_4000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_4001_5000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_5001_6000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_6001_7000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_7001_8000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_8001_9000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_9001_10000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_10001_11000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H4_2_gfblup_prediction_all,"H4_2_gfblup_prediction_all.rds")
+saveRDS(H4_2_gfblup_variances_all,"H4_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H4_3_gblup_prediction_all_1_1000=readRDS(file="H4_3_gblup_prediction_all_1_1000.rds")
+H4_3_gblup_prediction_all_1001_2000=readRDS(file="H4_3_gblup_prediction_all_1001_2000.rds")
+H4_3_gblup_prediction_all_2001_3000=readRDS(file="H4_3_gblup_prediction_all_2001_3000.rds")
+H4_3_gblup_prediction_all_3001_4000=readRDS(file="H4_3_gblup_prediction_all_3001_4000.rds")
+H4_3_gblup_prediction_all_4001_5000=readRDS(file="H4_3_gblup_prediction_all_4001_5000.rds")
+H4_3_gblup_prediction_all_5001_6000=readRDS(file="H4_3_gblup_prediction_all_5001_6000.rds")
+H4_3_gblup_prediction_all_6001_7000=readRDS(file="H4_3_gblup_prediction_all_6001_7000.rds")
+H4_3_gblup_prediction_all_7001_8000=readRDS(file="H4_3_gblup_prediction_all_7001_8000.rds")
+H4_3_gblup_prediction_all_8001_9000=readRDS(file="H4_3_gblup_prediction_all_8001_9000.rds")
+H4_3_gblup_prediction_all_9001_10000=readRDS(file="H4_3_gblup_prediction_all_9001_10000.rds")
+H4_3_gblup_prediction_all_10001_11000=readRDS(file="H4_3_gblup_prediction_all_10001_11000.rds")
+H4_3_gblup_prediction_all_11001_12419=readRDS(file="H4_3_gblup_prediction_all_11001_12419.rds")
+H4_3_gblup_prediction_all=c(H4_3_gblup_prediction_all_1_1000,H4_3_gblup_prediction_all_1001_2000,H4_3_gblup_prediction_all_2001_3000,H4_3_gblup_prediction_all_3001_4000,H4_3_gblup_prediction_all_4001_5000,H4_3_gblup_prediction_all_5001_6000,H4_3_gblup_prediction_all_6001_7000,H4_3_gblup_prediction_all_7001_8000,H4_3_gblup_prediction_all_8001_9000,H4_3_gblup_prediction_all_9001_10000,H4_3_gblup_prediction_all_10001_11000,H4_3_gblup_prediction_all_11001_12419)
+
+H4_3_gblup_variances_all_1_1000=readRDS(file="H4_3_gblup_variances_all_1_1000.rds")
+H4_3_gblup_variances_all_1001_2000=readRDS(file="H4_3_gblup_variances_all_1001_2000.rds")
+H4_3_gblup_variances_all_2001_3000=readRDS(file="H4_3_gblup_variances_all_2001_3000.rds")
+H4_3_gblup_variances_all_3001_4000=readRDS(file="H4_3_gblup_variances_all_3001_4000.rds")
+H4_3_gblup_variances_all_4001_5000=readRDS(file="H4_3_gblup_variances_all_4001_5000.rds")
+H4_3_gblup_variances_all_5001_6000=readRDS(file="H4_3_gblup_variances_all_5001_6000.rds")
+H4_3_gblup_variances_all_6001_7000=readRDS(file="H4_3_gblup_variances_all_6001_7000.rds")
+H4_3_gblup_variances_all_7001_8000=readRDS(file="H4_3_gblup_variances_all_7001_8000.rds")
+H4_3_gblup_variances_all_8001_9000=readRDS(file="H4_3_gblup_variances_all_8001_9000.rds")
+H4_3_gblup_variances_all_9001_10000=readRDS(file="H4_3_gblup_variances_all_9001_10000.rds")
+H4_3_gblup_variances_all_10001_11000=readRDS(file="H4_3_gblup_variances_all_10001_11000.rds")
+H4_3_gblup_variances_all_11001_12419=readRDS(file="H4_3_gblup_variances_all_11001_12419.rds")
+H4_3_gblup_variances_all=c(H4_3_gblup_variances_all_1_1000,H4_3_gblup_variances_all_1001_2000,H4_3_gblup_variances_all_2001_3000,H4_3_gblup_variances_all_3001_4000,H4_3_gblup_variances_all_4001_5000,H4_3_gblup_variances_all_5001_6000,H4_3_gblup_variances_all_6001_7000,H4_3_gblup_variances_all_7001_8000,H4_3_gblup_variances_all_8001_9000,H4_3_gblup_variances_all_9001_10000,H4_3_gblup_variances_all_10001_11000,H4_3_gblup_variances_all_11001_12419)
+
+saveRDS(H4_3_gblup_prediction_all,"H4_3_gblup_prediction_all.rds")
+saveRDS(H4_3_gblup_variances_all,"H4_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H4_3_gfblup_prediction_all_1_1000=readRDS(file="H4_3_gfblup_prediction_all_1_1000.rds")
+H4_3_gfblup_prediction_all_1001_2000=readRDS(file="H4_3_gfblup_prediction_all_1001_2000.rds")
+H4_3_gfblup_prediction_all_2001_3000=readRDS(file="H4_3_gfblup_prediction_all_2001_3000.rds")
+H4_3_gfblup_prediction_all_3001_4000=readRDS(file="H4_3_gfblup_prediction_all_3001_4000.rds")
+H4_3_gfblup_prediction_all_4001_5000=readRDS(file="H4_3_gfblup_prediction_all_4001_5000.rds")
+H4_3_gfblup_prediction_all_5001_6000=readRDS(file="H4_3_gfblup_prediction_all_5001_6000.rds")
+H4_3_gfblup_prediction_all_6001_7000=readRDS(file="H4_3_gfblup_prediction_all_6001_7000.rds")
+H4_3_gfblup_prediction_all_7001_8000=readRDS(file="H4_3_gfblup_prediction_all_7001_8000.rds")
+H4_3_gfblup_prediction_all_8001_9000=readRDS(file="H4_3_gfblup_prediction_all_8001_9000.rds")
+H4_3_gfblup_prediction_all_9001_10000=readRDS(file="H4_3_gfblup_prediction_all_9001_10000.rds")
+H4_3_gfblup_prediction_all_10001_11000=readRDS(file="H4_3_gfblup_prediction_all_10001_11000.rds")
+H4_3_gfblup_prediction_all_11001_12419=readRDS(file="H4_3_gfblup_prediction_all_11001_12419.rds")
+
+H4_3_gfblup_variances_all_1_1000=readRDS(file="H4_3_gfblup_variances_all_1_1000.rds")
+H4_3_gfblup_variances_all_1001_2000=readRDS(file="H4_3_gfblup_variances_all_1001_2000.rds")
+H4_3_gfblup_variances_all_2001_3000=readRDS(file="H4_3_gfblup_variances_all_2001_3000.rds")
+H4_3_gfblup_variances_all_3001_4000=readRDS(file="H4_3_gfblup_variances_all_3001_4000.rds")
+H4_3_gfblup_variances_all_4001_5000=readRDS(file="H4_3_gfblup_variances_all_4001_5000.rds")
+H4_3_gfblup_variances_all_5001_6000=readRDS(file="H4_3_gfblup_variances_all_5001_6000.rds")
+H4_3_gfblup_variances_all_6001_7000=readRDS(file="H4_3_gfblup_variances_all_6001_7000.rds")
+H4_3_gfblup_variances_all_7001_8000=readRDS(file="H4_3_gfblup_variances_all_7001_8000.rds")
+H4_3_gfblup_variances_all_8001_9000=readRDS(file="H4_3_gfblup_variances_all_8001_9000.rds")
+H4_3_gfblup_variances_all_9001_10000=readRDS(file="H4_3_gfblup_variances_all_9001_10000.rds")
+H4_3_gfblup_variances_all_10001_11000=readRDS(file="H4_3_gfblup_variances_all_10001_11000.rds")
+H4_3_gfblup_variances_all_11001_12419=readRDS(file="H4_3_gfblup_variances_all_11001_12419.rds")
+
+cycles=length(H4_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H4_3_gfblup_variances_all=rep(list(list()),cycles)
+H4_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_1_1000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_1001_2000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_2001_3000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_3001_4000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_4001_5000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_5001_6000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_6001_7000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_7001_8000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_8001_9000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_9001_10000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_10001_11000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_11001_12419[[r]])
+
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_1_1000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_1001_2000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_2001_3000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_3001_4000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_4001_5000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_5001_6000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_6001_7000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_7001_8000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_8001_9000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_9001_10000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_10001_11000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_11001_12419[[r]])
+}
+
+saveRDS(H4_3_gfblup_prediction_all,"H4_3_gfblup_prediction_all.rds")
+saveRDS(H4_3_gfblup_variances_all,"H4_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/code/using_COEX/psii/gblup_vs_gfblup_using_coexpression_analysis1.R b/code/using_COEX/psii/gblup_vs_gfblup_using_coexpression_analysis1.R
index cdf3923..a6f69d9 100644
--- a/code/using_COEX/psii/gblup_vs_gfblup_using_coexpression_analysis1.R
+++ b/code/using_COEX/psii/gblup_vs_gfblup_using_coexpression_analysis1.R
@@ -2,11 +2,27 @@
 ##################################################################################################################################
 #	A	N	A	L	Y	S	I	S
 ##################################################################################################################################
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_COEX/psii/8fold/")
-
-all_coexpression_clusters <-as.data.frame(read.table(file ="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE))
-coex_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers_number.rds")
-coex_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers.rds")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+setwd(paste0(wdir,"/",wd,"/8fold/"));
+##################################################################################################################################
+all_coexpression_clusters <-as.data.frame(read.table(file ="../data/priors/coexpression/ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE))
+coex_markers_number=readRDS(file="../data/priors/coexpression/coex_markers_number.rds")
+coex_markers=readRDS(file="../data/priors/coexpression/coex_markers.rds")
 ###################################################################################################################################
 H4_3_gblup_variances_all=readRDS(file="./H4_3_gblup_variances_all.rds")
 H4_3_gblup_prediction_all=readRDS(file="./H4_3_gblup_prediction_all.rds")
diff --git a/code/using_COEX/run_models.R b/code/using_COEX/run_models.R
index a53cc2a..48b1b1d 100644
--- a/code/using_COEX/run_models.R
+++ b/code/using_COEX/run_models.R
@@ -1,4 +1,23 @@
-cd /mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_COEX
+##################################################################################################################################
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+setwd(paste0(wdir,"/",wd));
+##################################################################################################################################
+
 Rscript psii/H1_1_1_1000.R
 Rscript psii/H1_1_10001_11000.R
 Rscript psii/H1_1_1001_2000.R
@@ -823,4 +842,4 @@ Rscript pla/T20_2_8001_9000.R
 Rscript pla/T20_2_9001_10000.R
 
 
-Rscript psii/8fold/combine.R
+Rscript pla/8fold/combine.R
diff --git a/code/using_GO/pla/8fold/combine.R b/code/using_GO/pla/8fold/combine.R
new file mode 100644
index 0000000..0be7b87
--- /dev/null
+++ b/code/using_GO/pla/8fold/combine.R
@@ -0,0 +1,3418 @@
+##################################################################################################################################
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+setwd(paste0(wdir,"/",wd));
+##################################################################################################################################
+T14_1_gblup_prediction_all_1_1000=readRDS(file="T14_1_gblup_prediction_all_1_1000.rds")
+T14_1_gblup_prediction_all_1001_2000=readRDS(file="T14_1_gblup_prediction_all_1001_2000.rds")
+T14_1_gblup_prediction_all_2001_3000=readRDS(file="T14_1_gblup_prediction_all_2001_3000.rds")
+T14_1_gblup_prediction_all_3001_4000=readRDS(file="T14_1_gblup_prediction_all_3001_4000.rds")
+T14_1_gblup_prediction_all_4001_5000=readRDS(file="T14_1_gblup_prediction_all_4001_5000.rds")
+T14_1_gblup_prediction_all_5001_6000=readRDS(file="T14_1_gblup_prediction_all_5001_6000.rds")
+T14_1_gblup_prediction_all_6001_7297=readRDS(file="T14_1_gblup_prediction_all_6001_7297.rds")
+T14_1_gblup_prediction_all=c(T14_1_gblup_prediction_all_1_1000,T14_1_gblup_prediction_all_1001_2000,T14_1_gblup_prediction_all_2001_3000,T14_1_gblup_prediction_all_3001_4000,T14_1_gblup_prediction_all_4001_5000,T14_1_gblup_prediction_all_5001_6000,T14_1_gblup_prediction_all_6001_7297)
+
+T14_1_gblup_variances_all_1_1000=readRDS(file="T14_1_gblup_variances_all_1_1000.rds")
+T14_1_gblup_variances_all_1001_2000=readRDS(file="T14_1_gblup_variances_all_1001_2000.rds")
+T14_1_gblup_variances_all_2001_3000=readRDS(file="T14_1_gblup_variances_all_2001_3000.rds")
+T14_1_gblup_variances_all_3001_4000=readRDS(file="T14_1_gblup_variances_all_3001_4000.rds")
+T14_1_gblup_variances_all_4001_5000=readRDS(file="T14_1_gblup_variances_all_4001_5000.rds")
+T14_1_gblup_variances_all_5001_6000=readRDS(file="T14_1_gblup_variances_all_5001_6000.rds")
+T14_1_gblup_variances_all_6001_7297=readRDS(file="T14_1_gblup_variances_all_6001_7297.rds")
+T14_1_gblup_variances_all=c(T14_1_gblup_variances_all_1_1000,T14_1_gblup_variances_all_1001_2000,T14_1_gblup_variances_all_2001_3000,T14_1_gblup_variances_all_3001_4000,T14_1_gblup_variances_all_4001_5000,T14_1_gblup_variances_all_5001_6000,T14_1_gblup_variances_all_6001_7297)
+
+saveRDS(T14_1_gblup_prediction_all,"T14_1_gblup_prediction_all.rds")
+saveRDS(T14_1_gblup_variances_all,"T14_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_1_gfblup_prediction_all_1_1000=readRDS(file="T14_1_gfblup_prediction_all_1_1000.rds")
+T14_1_gfblup_prediction_all_1001_2000=readRDS(file="T14_1_gfblup_prediction_all_1001_2000.rds")
+T14_1_gfblup_prediction_all_2001_3000=readRDS(file="T14_1_gfblup_prediction_all_2001_3000.rds")
+T14_1_gfblup_prediction_all_3001_4000=readRDS(file="T14_1_gfblup_prediction_all_3001_4000.rds")
+T14_1_gfblup_prediction_all_4001_5000=readRDS(file="T14_1_gfblup_prediction_all_4001_5000.rds")
+T14_1_gfblup_prediction_all_5001_6000=readRDS(file="T14_1_gfblup_prediction_all_5001_6000.rds")
+T14_1_gfblup_prediction_all_6001_7297=readRDS(file="T14_1_gfblup_prediction_all_6001_7297.rds")
+
+T14_1_gfblup_variances_all_1_1000=readRDS(file="T14_1_gfblup_variances_all_1_1000.rds")
+T14_1_gfblup_variances_all_1001_2000=readRDS(file="T14_1_gfblup_variances_all_1001_2000.rds")
+T14_1_gfblup_variances_all_2001_3000=readRDS(file="T14_1_gfblup_variances_all_2001_3000.rds")
+T14_1_gfblup_variances_all_3001_4000=readRDS(file="T14_1_gfblup_variances_all_3001_4000.rds")
+T14_1_gfblup_variances_all_4001_5000=readRDS(file="T14_1_gfblup_variances_all_4001_5000.rds")
+T14_1_gfblup_variances_all_5001_6000=readRDS(file="T14_1_gfblup_variances_all_5001_6000.rds")
+T14_1_gfblup_variances_all_6001_7297=readRDS(file="T14_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T14_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_1_gfblup_variances_all=rep(list(list()),cycles)
+T14_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_1_1000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_1001_2000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_2001_3000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_3001_4000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_4001_5000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_5001_6000[[r]])
+	T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_6001_7297[[r]])
+
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_1_1000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_1001_2000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_2001_3000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_3001_4000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_4001_5000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_5001_6000[[r]])
+	T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T14_1_gfblup_prediction_all,"T14_1_gfblup_prediction_all.rds")
+saveRDS(T14_1_gfblup_variances_all,"T14_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_2_gblup_prediction_all_1_1000=readRDS(file="T14_2_gblup_prediction_all_1_1000.rds")
+T14_2_gblup_prediction_all_1001_2000=readRDS(file="T14_2_gblup_prediction_all_1001_2000.rds")
+T14_2_gblup_prediction_all_2001_3000=readRDS(file="T14_2_gblup_prediction_all_2001_3000.rds")
+T14_2_gblup_prediction_all_3001_4000=readRDS(file="T14_2_gblup_prediction_all_3001_4000.rds")
+T14_2_gblup_prediction_all_4001_5000=readRDS(file="T14_2_gblup_prediction_all_4001_5000.rds")
+T14_2_gblup_prediction_all_5001_6000=readRDS(file="T14_2_gblup_prediction_all_5001_6000.rds")
+T14_2_gblup_prediction_all_6001_7297=readRDS(file="T14_2_gblup_prediction_all_6001_7297.rds")
+T14_2_gblup_prediction_all=c(T14_2_gblup_prediction_all_1_1000,T14_2_gblup_prediction_all_1001_2000,T14_2_gblup_prediction_all_2001_3000,T14_2_gblup_prediction_all_3001_4000,T14_2_gblup_prediction_all_4001_5000,T14_2_gblup_prediction_all_5001_6000,T14_2_gblup_prediction_all_6001_7297)
+
+T14_2_gblup_variances_all_1_1000=readRDS(file="T14_2_gblup_variances_all_1_1000.rds")
+T14_2_gblup_variances_all_1001_2000=readRDS(file="T14_2_gblup_variances_all_1001_2000.rds")
+T14_2_gblup_variances_all_2001_3000=readRDS(file="T14_2_gblup_variances_all_2001_3000.rds")
+T14_2_gblup_variances_all_3001_4000=readRDS(file="T14_2_gblup_variances_all_3001_4000.rds")
+T14_2_gblup_variances_all_4001_5000=readRDS(file="T14_2_gblup_variances_all_4001_5000.rds")
+T14_2_gblup_variances_all_5001_6000=readRDS(file="T14_2_gblup_variances_all_5001_6000.rds")
+T14_2_gblup_variances_all_6001_7297=readRDS(file="T14_2_gblup_variances_all_6001_7297.rds")
+T14_2_gblup_variances_all=c(T14_2_gblup_variances_all_1_1000,T14_2_gblup_variances_all_1001_2000,T14_2_gblup_variances_all_2001_3000,T14_2_gblup_variances_all_3001_4000,T14_2_gblup_variances_all_4001_5000,T14_2_gblup_variances_all_5001_6000,T14_2_gblup_variances_all_6001_7297)
+
+saveRDS(T14_2_gblup_prediction_all,"T14_2_gblup_prediction_all.rds")
+saveRDS(T14_2_gblup_variances_all,"T14_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_2_gfblup_prediction_all_1_1000=readRDS(file="T14_2_gfblup_prediction_all_1_1000.rds")
+T14_2_gfblup_prediction_all_1001_2000=readRDS(file="T14_2_gfblup_prediction_all_1001_2000.rds")
+T14_2_gfblup_prediction_all_2001_3000=readRDS(file="T14_2_gfblup_prediction_all_2001_3000.rds")
+T14_2_gfblup_prediction_all_3001_4000=readRDS(file="T14_2_gfblup_prediction_all_3001_4000.rds")
+T14_2_gfblup_prediction_all_4001_5000=readRDS(file="T14_2_gfblup_prediction_all_4001_5000.rds")
+T14_2_gfblup_prediction_all_5001_6000=readRDS(file="T14_2_gfblup_prediction_all_5001_6000.rds")
+T14_2_gfblup_prediction_all_6001_7297=readRDS(file="T14_2_gfblup_prediction_all_6001_7297.rds")
+
+T14_2_gfblup_variances_all_1_1000=readRDS(file="T14_2_gfblup_variances_all_1_1000.rds")
+T14_2_gfblup_variances_all_1001_2000=readRDS(file="T14_2_gfblup_variances_all_1001_2000.rds")
+T14_2_gfblup_variances_all_2001_3000=readRDS(file="T14_2_gfblup_variances_all_2001_3000.rds")
+T14_2_gfblup_variances_all_3001_4000=readRDS(file="T14_2_gfblup_variances_all_3001_4000.rds")
+T14_2_gfblup_variances_all_4001_5000=readRDS(file="T14_2_gfblup_variances_all_4001_5000.rds")
+T14_2_gfblup_variances_all_5001_6000=readRDS(file="T14_2_gfblup_variances_all_5001_6000.rds")
+T14_2_gfblup_variances_all_6001_7297=readRDS(file="T14_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T14_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_2_gfblup_variances_all=rep(list(list()),cycles)
+T14_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_1_1000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_1001_2000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_2001_3000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_3001_4000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_4001_5000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_5001_6000[[r]])
+	T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_6001_7297[[r]])
+
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_1_1000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_1001_2000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_2001_3000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_3001_4000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_4001_5000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_5001_6000[[r]])
+	T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T14_2_gfblup_prediction_all,"T14_2_gfblup_prediction_all.rds")
+saveRDS(T14_2_gfblup_variances_all,"T14_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_3_gblup_prediction_all_1_1000=readRDS(file="T14_3_gblup_prediction_all_1_1000.rds")
+T14_3_gblup_prediction_all_1001_2000=readRDS(file="T14_3_gblup_prediction_all_1001_2000.rds")
+T14_3_gblup_prediction_all_2001_3000=readRDS(file="T14_3_gblup_prediction_all_2001_3000.rds")
+T14_3_gblup_prediction_all_3001_4000=readRDS(file="T14_3_gblup_prediction_all_3001_4000.rds")
+T14_3_gblup_prediction_all_4001_5000=readRDS(file="T14_3_gblup_prediction_all_4001_5000.rds")
+T14_3_gblup_prediction_all_5001_6000=readRDS(file="T14_3_gblup_prediction_all_5001_6000.rds")
+T14_3_gblup_prediction_all_6001_7297=readRDS(file="T14_3_gblup_prediction_all_6001_7297.rds")
+T14_3_gblup_prediction_all=c(T14_3_gblup_prediction_all_1_1000,T14_3_gblup_prediction_all_1001_2000,T14_3_gblup_prediction_all_2001_3000,T14_3_gblup_prediction_all_3001_4000,T14_3_gblup_prediction_all_4001_5000,T14_3_gblup_prediction_all_5001_6000,T14_3_gblup_prediction_all_6001_7297)
+
+T14_3_gblup_variances_all_1_1000=readRDS(file="T14_3_gblup_variances_all_1_1000.rds")
+T14_3_gblup_variances_all_1001_2000=readRDS(file="T14_3_gblup_variances_all_1001_2000.rds")
+T14_3_gblup_variances_all_2001_3000=readRDS(file="T14_3_gblup_variances_all_2001_3000.rds")
+T14_3_gblup_variances_all_3001_4000=readRDS(file="T14_3_gblup_variances_all_3001_4000.rds")
+T14_3_gblup_variances_all_4001_5000=readRDS(file="T14_3_gblup_variances_all_4001_5000.rds")
+T14_3_gblup_variances_all_5001_6000=readRDS(file="T14_3_gblup_variances_all_5001_6000.rds")
+T14_3_gblup_variances_all_6001_7297=readRDS(file="T14_3_gblup_variances_all_6001_7297.rds")
+T14_3_gblup_variances_all=c(T14_3_gblup_variances_all_1_1000,T14_3_gblup_variances_all_1001_2000,T14_3_gblup_variances_all_2001_3000,T14_3_gblup_variances_all_3001_4000,T14_3_gblup_variances_all_4001_5000,T14_3_gblup_variances_all_5001_6000,T14_3_gblup_variances_all_6001_7297)
+
+saveRDS(T14_3_gblup_prediction_all,"T14_3_gblup_prediction_all.rds")
+saveRDS(T14_3_gblup_variances_all,"T14_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_3_gfblup_prediction_all_1_1000=readRDS(file="T14_3_gfblup_prediction_all_1_1000.rds")
+T14_3_gfblup_prediction_all_1001_2000=readRDS(file="T14_3_gfblup_prediction_all_1001_2000.rds")
+T14_3_gfblup_prediction_all_2001_3000=readRDS(file="T14_3_gfblup_prediction_all_2001_3000.rds")
+T14_3_gfblup_prediction_all_3001_4000=readRDS(file="T14_3_gfblup_prediction_all_3001_4000.rds")
+T14_3_gfblup_prediction_all_4001_5000=readRDS(file="T14_3_gfblup_prediction_all_4001_5000.rds")
+T14_3_gfblup_prediction_all_5001_6000=readRDS(file="T14_3_gfblup_prediction_all_5001_6000.rds")
+T14_3_gfblup_prediction_all_6001_7297=readRDS(file="T14_3_gfblup_prediction_all_6001_7297.rds")
+
+T14_3_gfblup_variances_all_1_1000=readRDS(file="T14_3_gfblup_variances_all_1_1000.rds")
+T14_3_gfblup_variances_all_1001_2000=readRDS(file="T14_3_gfblup_variances_all_1001_2000.rds")
+T14_3_gfblup_variances_all_2001_3000=readRDS(file="T14_3_gfblup_variances_all_2001_3000.rds")
+T14_3_gfblup_variances_all_3001_4000=readRDS(file="T14_3_gfblup_variances_all_3001_4000.rds")
+T14_3_gfblup_variances_all_4001_5000=readRDS(file="T14_3_gfblup_variances_all_4001_5000.rds")
+T14_3_gfblup_variances_all_5001_6000=readRDS(file="T14_3_gfblup_variances_all_5001_6000.rds")
+T14_3_gfblup_variances_all_6001_7297=readRDS(file="T14_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T14_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_3_gfblup_variances_all=rep(list(list()),cycles)
+T14_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_1_1000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_1001_2000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_2001_3000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_3001_4000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_4001_5000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_5001_6000[[r]])
+	T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_6001_7297[[r]])
+
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_1_1000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_1001_2000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_2001_3000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_3001_4000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_4001_5000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_5001_6000[[r]])
+	T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T14_3_gfblup_prediction_all,"T14_3_gfblup_prediction_all.rds")
+saveRDS(T14_3_gfblup_variances_all,"T14_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_4_gblup_prediction_all_1_1000=readRDS(file="T14_4_gblup_prediction_all_1_1000.rds")
+T14_4_gblup_prediction_all_1001_2000=readRDS(file="T14_4_gblup_prediction_all_1001_2000.rds")
+T14_4_gblup_prediction_all_2001_3000=readRDS(file="T14_4_gblup_prediction_all_2001_3000.rds")
+T14_4_gblup_prediction_all_3001_4000=readRDS(file="T14_4_gblup_prediction_all_3001_4000.rds")
+T14_4_gblup_prediction_all_4001_5000=readRDS(file="T14_4_gblup_prediction_all_4001_5000.rds")
+T14_4_gblup_prediction_all_5001_6000=readRDS(file="T14_4_gblup_prediction_all_5001_6000.rds")
+T14_4_gblup_prediction_all_6001_7297=readRDS(file="T14_4_gblup_prediction_all_6001_7297.rds")
+T14_4_gblup_prediction_all=c(T14_4_gblup_prediction_all_1_1000,T14_4_gblup_prediction_all_1001_2000,T14_4_gblup_prediction_all_2001_3000,T14_4_gblup_prediction_all_3001_4000,T14_4_gblup_prediction_all_4001_5000,T14_4_gblup_prediction_all_5001_6000,T14_4_gblup_prediction_all_6001_7297)
+
+T14_4_gblup_variances_all_1_1000=readRDS(file="T14_4_gblup_variances_all_1_1000.rds")
+T14_4_gblup_variances_all_1001_2000=readRDS(file="T14_4_gblup_variances_all_1001_2000.rds")
+T14_4_gblup_variances_all_2001_3000=readRDS(file="T14_4_gblup_variances_all_2001_3000.rds")
+T14_4_gblup_variances_all_3001_4000=readRDS(file="T14_4_gblup_variances_all_3001_4000.rds")
+T14_4_gblup_variances_all_4001_5000=readRDS(file="T14_4_gblup_variances_all_4001_5000.rds")
+T14_4_gblup_variances_all_5001_6000=readRDS(file="T14_4_gblup_variances_all_5001_6000.rds")
+T14_4_gblup_variances_all_6001_7297=readRDS(file="T14_4_gblup_variances_all_6001_7297.rds")
+T14_4_gblup_variances_all=c(T14_4_gblup_variances_all_1_1000,T14_4_gblup_variances_all_1001_2000,T14_4_gblup_variances_all_2001_3000,T14_4_gblup_variances_all_3001_4000,T14_4_gblup_variances_all_4001_5000,T14_4_gblup_variances_all_5001_6000,T14_4_gblup_variances_all_6001_7297)
+
+saveRDS(T14_4_gblup_prediction_all,"T14_4_gblup_prediction_all.rds")
+saveRDS(T14_4_gblup_variances_all,"T14_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_4_gfblup_prediction_all_1_1000=readRDS(file="T14_4_gfblup_prediction_all_1_1000.rds")
+T14_4_gfblup_prediction_all_1001_2000=readRDS(file="T14_4_gfblup_prediction_all_1001_2000.rds")
+T14_4_gfblup_prediction_all_2001_3000=readRDS(file="T14_4_gfblup_prediction_all_2001_3000.rds")
+T14_4_gfblup_prediction_all_3001_4000=readRDS(file="T14_4_gfblup_prediction_all_3001_4000.rds")
+T14_4_gfblup_prediction_all_4001_5000=readRDS(file="T14_4_gfblup_prediction_all_4001_5000.rds")
+T14_4_gfblup_prediction_all_5001_6000=readRDS(file="T14_4_gfblup_prediction_all_5001_6000.rds")
+T14_4_gfblup_prediction_all_6001_7297=readRDS(file="T14_4_gfblup_prediction_all_6001_7297.rds")
+
+T14_4_gfblup_variances_all_1_1000=readRDS(file="T14_4_gfblup_variances_all_1_1000.rds")
+T14_4_gfblup_variances_all_1001_2000=readRDS(file="T14_4_gfblup_variances_all_1001_2000.rds")
+T14_4_gfblup_variances_all_2001_3000=readRDS(file="T14_4_gfblup_variances_all_2001_3000.rds")
+T14_4_gfblup_variances_all_3001_4000=readRDS(file="T14_4_gfblup_variances_all_3001_4000.rds")
+T14_4_gfblup_variances_all_4001_5000=readRDS(file="T14_4_gfblup_variances_all_4001_5000.rds")
+T14_4_gfblup_variances_all_5001_6000=readRDS(file="T14_4_gfblup_variances_all_5001_6000.rds")
+T14_4_gfblup_variances_all_6001_7297=readRDS(file="T14_4_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T14_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_4_gfblup_variances_all=rep(list(list()),cycles)
+T14_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_1_1000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_1001_2000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_2001_3000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_3001_4000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_4001_5000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_5001_6000[[r]])
+	T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_6001_7297[[r]])
+
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_1_1000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_1001_2000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_2001_3000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_3001_4000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_4001_5000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_5001_6000[[r]])
+	T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T14_4_gfblup_prediction_all,"T14_4_gfblup_prediction_all.rds")
+saveRDS(T14_4_gfblup_variances_all,"T14_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_5_gblup_prediction_all_1_1000=readRDS(file="T14_5_gblup_prediction_all_1_1000.rds")
+T14_5_gblup_prediction_all_1001_2000=readRDS(file="T14_5_gblup_prediction_all_1001_2000.rds")
+T14_5_gblup_prediction_all_2001_3000=readRDS(file="T14_5_gblup_prediction_all_2001_3000.rds")
+T14_5_gblup_prediction_all_3001_4000=readRDS(file="T14_5_gblup_prediction_all_3001_4000.rds")
+T14_5_gblup_prediction_all_4001_5000=readRDS(file="T14_5_gblup_prediction_all_4001_5000.rds")
+T14_5_gblup_prediction_all_5001_6000=readRDS(file="T14_5_gblup_prediction_all_5001_6000.rds")
+T14_5_gblup_prediction_all_6001_7297=readRDS(file="T14_5_gblup_prediction_all_6001_7297.rds")
+T14_5_gblup_prediction_all=c(T14_5_gblup_prediction_all_1_1000,T14_5_gblup_prediction_all_1001_2000,T14_5_gblup_prediction_all_2001_3000,T14_5_gblup_prediction_all_3001_4000,T14_5_gblup_prediction_all_4001_5000,T14_5_gblup_prediction_all_5001_6000,T14_5_gblup_prediction_all_6001_7297)
+
+T14_5_gblup_variances_all_1_1000=readRDS(file="T14_5_gblup_variances_all_1_1000.rds")
+T14_5_gblup_variances_all_1001_2000=readRDS(file="T14_5_gblup_variances_all_1001_2000.rds")
+T14_5_gblup_variances_all_2001_3000=readRDS(file="T14_5_gblup_variances_all_2001_3000.rds")
+T14_5_gblup_variances_all_3001_4000=readRDS(file="T14_5_gblup_variances_all_3001_4000.rds")
+T14_5_gblup_variances_all_4001_5000=readRDS(file="T14_5_gblup_variances_all_4001_5000.rds")
+T14_5_gblup_variances_all_5001_6000=readRDS(file="T14_5_gblup_variances_all_5001_6000.rds")
+T14_5_gblup_variances_all_6001_7297=readRDS(file="T14_5_gblup_variances_all_6001_7297.rds")
+T14_5_gblup_variances_all=c(T14_5_gblup_variances_all_1_1000,T14_5_gblup_variances_all_1001_2000,T14_5_gblup_variances_all_2001_3000,T14_5_gblup_variances_all_3001_4000,T14_5_gblup_variances_all_4001_5000,T14_5_gblup_variances_all_5001_6000,T14_5_gblup_variances_all_6001_7297)
+
+saveRDS(T14_5_gblup_prediction_all,"T14_5_gblup_prediction_all.rds")
+saveRDS(T14_5_gblup_variances_all,"T14_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_5_gfblup_prediction_all_1_1000=readRDS(file="T14_5_gfblup_prediction_all_1_1000.rds")
+T14_5_gfblup_prediction_all_1001_2000=readRDS(file="T14_5_gfblup_prediction_all_1001_2000.rds")
+T14_5_gfblup_prediction_all_2001_3000=readRDS(file="T14_5_gfblup_prediction_all_2001_3000.rds")
+T14_5_gfblup_prediction_all_3001_4000=readRDS(file="T14_5_gfblup_prediction_all_3001_4000.rds")
+T14_5_gfblup_prediction_all_4001_5000=readRDS(file="T14_5_gfblup_prediction_all_4001_5000.rds")
+T14_5_gfblup_prediction_all_5001_6000=readRDS(file="T14_5_gfblup_prediction_all_5001_6000.rds")
+T14_5_gfblup_prediction_all_6001_7297=readRDS(file="T14_5_gfblup_prediction_all_6001_7297.rds")
+
+T14_5_gfblup_variances_all_1_1000=readRDS(file="T14_5_gfblup_variances_all_1_1000.rds")
+T14_5_gfblup_variances_all_1001_2000=readRDS(file="T14_5_gfblup_variances_all_1001_2000.rds")
+T14_5_gfblup_variances_all_2001_3000=readRDS(file="T14_5_gfblup_variances_all_2001_3000.rds")
+T14_5_gfblup_variances_all_3001_4000=readRDS(file="T14_5_gfblup_variances_all_3001_4000.rds")
+T14_5_gfblup_variances_all_4001_5000=readRDS(file="T14_5_gfblup_variances_all_4001_5000.rds")
+T14_5_gfblup_variances_all_5001_6000=readRDS(file="T14_5_gfblup_variances_all_5001_6000.rds")
+T14_5_gfblup_variances_all_6001_7297=readRDS(file="T14_5_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T14_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_5_gfblup_variances_all=rep(list(list()),cycles)
+T14_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_1_1000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_1001_2000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_2001_3000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_3001_4000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_4001_5000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_5001_6000[[r]])
+	T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_6001_7297[[r]])
+
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_1_1000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_1001_2000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_2001_3000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_3001_4000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_4001_5000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_5001_6000[[r]])
+	T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T14_5_gfblup_prediction_all,"T14_5_gfblup_prediction_all.rds")
+saveRDS(T14_5_gfblup_variances_all,"T14_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_6_gblup_prediction_all_1_1000=readRDS(file="T14_6_gblup_prediction_all_1_1000.rds")
+T14_6_gblup_prediction_all_1001_2000=readRDS(file="T14_6_gblup_prediction_all_1001_2000.rds")
+T14_6_gblup_prediction_all_2001_3000=readRDS(file="T14_6_gblup_prediction_all_2001_3000.rds")
+T14_6_gblup_prediction_all_3001_4000=readRDS(file="T14_6_gblup_prediction_all_3001_4000.rds")
+T14_6_gblup_prediction_all_4001_5000=readRDS(file="T14_6_gblup_prediction_all_4001_5000.rds")
+T14_6_gblup_prediction_all_5001_6000=readRDS(file="T14_6_gblup_prediction_all_5001_6000.rds")
+T14_6_gblup_prediction_all_6001_7297=readRDS(file="T14_6_gblup_prediction_all_6001_7297.rds")
+T14_6_gblup_prediction_all=c(T14_6_gblup_prediction_all_1_1000,T14_6_gblup_prediction_all_1001_2000,T14_6_gblup_prediction_all_2001_3000,T14_6_gblup_prediction_all_3001_4000,T14_6_gblup_prediction_all_4001_5000,T14_6_gblup_prediction_all_5001_6000,T14_6_gblup_prediction_all_6001_7297)
+
+T14_6_gblup_variances_all_1_1000=readRDS(file="T14_6_gblup_variances_all_1_1000.rds")
+T14_6_gblup_variances_all_1001_2000=readRDS(file="T14_6_gblup_variances_all_1001_2000.rds")
+T14_6_gblup_variances_all_2001_3000=readRDS(file="T14_6_gblup_variances_all_2001_3000.rds")
+T14_6_gblup_variances_all_3001_4000=readRDS(file="T14_6_gblup_variances_all_3001_4000.rds")
+T14_6_gblup_variances_all_4001_5000=readRDS(file="T14_6_gblup_variances_all_4001_5000.rds")
+T14_6_gblup_variances_all_5001_6000=readRDS(file="T14_6_gblup_variances_all_5001_6000.rds")
+T14_6_gblup_variances_all_6001_7297=readRDS(file="T14_6_gblup_variances_all_6001_7297.rds")
+T14_6_gblup_variances_all=c(T14_6_gblup_variances_all_1_1000,T14_6_gblup_variances_all_1001_2000,T14_6_gblup_variances_all_2001_3000,T14_6_gblup_variances_all_3001_4000,T14_6_gblup_variances_all_4001_5000,T14_6_gblup_variances_all_5001_6000,T14_6_gblup_variances_all_6001_7297)
+
+saveRDS(T14_6_gblup_prediction_all,"T14_6_gblup_prediction_all.rds")
+saveRDS(T14_6_gblup_variances_all,"T14_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_6_gfblup_prediction_all_1_1000=readRDS(file="T14_6_gfblup_prediction_all_1_1000.rds")
+T14_6_gfblup_prediction_all_1001_2000=readRDS(file="T14_6_gfblup_prediction_all_1001_2000.rds")
+T14_6_gfblup_prediction_all_2001_3000=readRDS(file="T14_6_gfblup_prediction_all_2001_3000.rds")
+T14_6_gfblup_prediction_all_3001_4000=readRDS(file="T14_6_gfblup_prediction_all_3001_4000.rds")
+T14_6_gfblup_prediction_all_4001_5000=readRDS(file="T14_6_gfblup_prediction_all_4001_5000.rds")
+T14_6_gfblup_prediction_all_5001_6000=readRDS(file="T14_6_gfblup_prediction_all_5001_6000.rds")
+T14_6_gfblup_prediction_all_6001_7297=readRDS(file="T14_6_gfblup_prediction_all_6001_7297.rds")
+
+T14_6_gfblup_variances_all_1_1000=readRDS(file="T14_6_gfblup_variances_all_1_1000.rds")
+T14_6_gfblup_variances_all_1001_2000=readRDS(file="T14_6_gfblup_variances_all_1001_2000.rds")
+T14_6_gfblup_variances_all_2001_3000=readRDS(file="T14_6_gfblup_variances_all_2001_3000.rds")
+T14_6_gfblup_variances_all_3001_4000=readRDS(file="T14_6_gfblup_variances_all_3001_4000.rds")
+T14_6_gfblup_variances_all_4001_5000=readRDS(file="T14_6_gfblup_variances_all_4001_5000.rds")
+T14_6_gfblup_variances_all_5001_6000=readRDS(file="T14_6_gfblup_variances_all_5001_6000.rds")
+T14_6_gfblup_variances_all_6001_7297=readRDS(file="T14_6_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T14_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_6_gfblup_variances_all=rep(list(list()),cycles)
+T14_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_1_1000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_1001_2000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_2001_3000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_3001_4000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_4001_5000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_5001_6000[[r]])
+	T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_6001_7297[[r]])
+
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_1_1000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_1001_2000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_2001_3000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_3001_4000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_4001_5000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_5001_6000[[r]])
+	T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T14_6_gfblup_prediction_all,"T14_6_gfblup_prediction_all.rds")
+saveRDS(T14_6_gfblup_variances_all,"T14_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_7_gblup_prediction_all_1_1000=readRDS(file="T14_7_gblup_prediction_all_1_1000.rds")
+T14_7_gblup_prediction_all_1001_2000=readRDS(file="T14_7_gblup_prediction_all_1001_2000.rds")
+T14_7_gblup_prediction_all_2001_3000=readRDS(file="T14_7_gblup_prediction_all_2001_3000.rds")
+T14_7_gblup_prediction_all_3001_4000=readRDS(file="T14_7_gblup_prediction_all_3001_4000.rds")
+T14_7_gblup_prediction_all_4001_5000=readRDS(file="T14_7_gblup_prediction_all_4001_5000.rds")
+T14_7_gblup_prediction_all_5001_6000=readRDS(file="T14_7_gblup_prediction_all_5001_6000.rds")
+T14_7_gblup_prediction_all_6001_7297=readRDS(file="T14_7_gblup_prediction_all_6001_7297.rds")
+T14_7_gblup_prediction_all=c(T14_7_gblup_prediction_all_1_1000,T14_7_gblup_prediction_all_1001_2000,T14_7_gblup_prediction_all_2001_3000,T14_7_gblup_prediction_all_3001_4000,T14_7_gblup_prediction_all_4001_5000,T14_7_gblup_prediction_all_5001_6000,T14_7_gblup_prediction_all_6001_7297)
+
+T14_7_gblup_variances_all_1_1000=readRDS(file="T14_7_gblup_variances_all_1_1000.rds")
+T14_7_gblup_variances_all_1001_2000=readRDS(file="T14_7_gblup_variances_all_1001_2000.rds")
+T14_7_gblup_variances_all_2001_3000=readRDS(file="T14_7_gblup_variances_all_2001_3000.rds")
+T14_7_gblup_variances_all_3001_4000=readRDS(file="T14_7_gblup_variances_all_3001_4000.rds")
+T14_7_gblup_variances_all_4001_5000=readRDS(file="T14_7_gblup_variances_all_4001_5000.rds")
+T14_7_gblup_variances_all_5001_6000=readRDS(file="T14_7_gblup_variances_all_5001_6000.rds")
+T14_7_gblup_variances_all_6001_7297=readRDS(file="T14_7_gblup_variances_all_6001_7297.rds")
+T14_7_gblup_variances_all=c(T14_7_gblup_variances_all_1_1000,T14_7_gblup_variances_all_1001_2000,T14_7_gblup_variances_all_2001_3000,T14_7_gblup_variances_all_3001_4000,T14_7_gblup_variances_all_4001_5000,T14_7_gblup_variances_all_5001_6000,T14_7_gblup_variances_all_6001_7297)
+
+saveRDS(T14_7_gblup_prediction_all,"T14_7_gblup_prediction_all.rds")
+saveRDS(T14_7_gblup_variances_all,"T14_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_7_gfblup_prediction_all_1_1000=readRDS(file="T14_7_gfblup_prediction_all_1_1000.rds")
+T14_7_gfblup_prediction_all_1001_2000=readRDS(file="T14_7_gfblup_prediction_all_1001_2000.rds")
+T14_7_gfblup_prediction_all_2001_3000=readRDS(file="T14_7_gfblup_prediction_all_2001_3000.rds")
+T14_7_gfblup_prediction_all_3001_4000=readRDS(file="T14_7_gfblup_prediction_all_3001_4000.rds")
+T14_7_gfblup_prediction_all_4001_5000=readRDS(file="T14_7_gfblup_prediction_all_4001_5000.rds")
+T14_7_gfblup_prediction_all_5001_6000=readRDS(file="T14_7_gfblup_prediction_all_5001_6000.rds")
+T14_7_gfblup_prediction_all_6001_7297=readRDS(file="T14_7_gfblup_prediction_all_6001_7297.rds")
+
+T14_7_gfblup_variances_all_1_1000=readRDS(file="T14_7_gfblup_variances_all_1_1000.rds")
+T14_7_gfblup_variances_all_1001_2000=readRDS(file="T14_7_gfblup_variances_all_1001_2000.rds")
+T14_7_gfblup_variances_all_2001_3000=readRDS(file="T14_7_gfblup_variances_all_2001_3000.rds")
+T14_7_gfblup_variances_all_3001_4000=readRDS(file="T14_7_gfblup_variances_all_3001_4000.rds")
+T14_7_gfblup_variances_all_4001_5000=readRDS(file="T14_7_gfblup_variances_all_4001_5000.rds")
+T14_7_gfblup_variances_all_5001_6000=readRDS(file="T14_7_gfblup_variances_all_5001_6000.rds")
+T14_7_gfblup_variances_all_6001_7297=readRDS(file="T14_7_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T14_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_7_gfblup_variances_all=rep(list(list()),cycles)
+T14_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_1_1000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_1001_2000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_2001_3000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_3001_4000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_4001_5000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_5001_6000[[r]])
+	T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_6001_7297[[r]])
+
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_1_1000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_1001_2000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_2001_3000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_3001_4000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_4001_5000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_5001_6000[[r]])
+	T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T14_7_gfblup_prediction_all,"T14_7_gfblup_prediction_all.rds")
+saveRDS(T14_7_gfblup_variances_all,"T14_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_8_gblup_prediction_all_1_1000=readRDS(file="T14_8_gblup_prediction_all_1_1000.rds")
+T14_8_gblup_prediction_all_1001_2000=readRDS(file="T14_8_gblup_prediction_all_1001_2000.rds")
+T14_8_gblup_prediction_all_2001_3000=readRDS(file="T14_8_gblup_prediction_all_2001_3000.rds")
+T14_8_gblup_prediction_all_3001_4000=readRDS(file="T14_8_gblup_prediction_all_3001_4000.rds")
+T14_8_gblup_prediction_all_4001_5000=readRDS(file="T14_8_gblup_prediction_all_4001_5000.rds")
+T14_8_gblup_prediction_all_5001_6000=readRDS(file="T14_8_gblup_prediction_all_5001_6000.rds")
+T14_8_gblup_prediction_all_6001_7297=readRDS(file="T14_8_gblup_prediction_all_6001_7297.rds")
+T14_8_gblup_prediction_all=c(T14_8_gblup_prediction_all_1_1000,T14_8_gblup_prediction_all_1001_2000,T14_8_gblup_prediction_all_2001_3000,T14_8_gblup_prediction_all_3001_4000,T14_8_gblup_prediction_all_4001_5000,T14_8_gblup_prediction_all_5001_6000,T14_8_gblup_prediction_all_6001_7297)
+
+T14_8_gblup_variances_all_1_1000=readRDS(file="T14_8_gblup_variances_all_1_1000.rds")
+T14_8_gblup_variances_all_1001_2000=readRDS(file="T14_8_gblup_variances_all_1001_2000.rds")
+T14_8_gblup_variances_all_2001_3000=readRDS(file="T14_8_gblup_variances_all_2001_3000.rds")
+T14_8_gblup_variances_all_3001_4000=readRDS(file="T14_8_gblup_variances_all_3001_4000.rds")
+T14_8_gblup_variances_all_4001_5000=readRDS(file="T14_8_gblup_variances_all_4001_5000.rds")
+T14_8_gblup_variances_all_5001_6000=readRDS(file="T14_8_gblup_variances_all_5001_6000.rds")
+T14_8_gblup_variances_all_6001_7297=readRDS(file="T14_8_gblup_variances_all_6001_7297.rds")
+T14_8_gblup_variances_all=c(T14_8_gblup_variances_all_1_1000,T14_8_gblup_variances_all_1001_2000,T14_8_gblup_variances_all_2001_3000,T14_8_gblup_variances_all_3001_4000,T14_8_gblup_variances_all_4001_5000,T14_8_gblup_variances_all_5001_6000,T14_8_gblup_variances_all_6001_7297)
+
+saveRDS(T14_8_gblup_prediction_all,"T14_8_gblup_prediction_all.rds")
+saveRDS(T14_8_gblup_variances_all,"T14_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T14_8_gfblup_prediction_all_1_1000=readRDS(file="T14_8_gfblup_prediction_all_1_1000.rds")
+T14_8_gfblup_prediction_all_1001_2000=readRDS(file="T14_8_gfblup_prediction_all_1001_2000.rds")
+T14_8_gfblup_prediction_all_2001_3000=readRDS(file="T14_8_gfblup_prediction_all_2001_3000.rds")
+T14_8_gfblup_prediction_all_3001_4000=readRDS(file="T14_8_gfblup_prediction_all_3001_4000.rds")
+T14_8_gfblup_prediction_all_4001_5000=readRDS(file="T14_8_gfblup_prediction_all_4001_5000.rds")
+T14_8_gfblup_prediction_all_5001_6000=readRDS(file="T14_8_gfblup_prediction_all_5001_6000.rds")
+T14_8_gfblup_prediction_all_6001_7297=readRDS(file="T14_8_gfblup_prediction_all_6001_7297.rds")
+
+T14_8_gfblup_variances_all_1_1000=readRDS(file="T14_8_gfblup_variances_all_1_1000.rds")
+T14_8_gfblup_variances_all_1001_2000=readRDS(file="T14_8_gfblup_variances_all_1001_2000.rds")
+T14_8_gfblup_variances_all_2001_3000=readRDS(file="T14_8_gfblup_variances_all_2001_3000.rds")
+T14_8_gfblup_variances_all_3001_4000=readRDS(file="T14_8_gfblup_variances_all_3001_4000.rds")
+T14_8_gfblup_variances_all_4001_5000=readRDS(file="T14_8_gfblup_variances_all_4001_5000.rds")
+T14_8_gfblup_variances_all_5001_6000=readRDS(file="T14_8_gfblup_variances_all_5001_6000.rds")
+T14_8_gfblup_variances_all_6001_7297=readRDS(file="T14_8_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T14_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T14_8_gfblup_variances_all=rep(list(list()),cycles)
+T14_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_1_1000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_1001_2000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_2001_3000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_3001_4000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_4001_5000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_5001_6000[[r]])
+	T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_6001_7297[[r]])
+
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_1_1000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_1001_2000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_2001_3000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_3001_4000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_4001_5000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_5001_6000[[r]])
+	T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T14_8_gfblup_prediction_all,"T14_8_gfblup_prediction_all.rds")
+saveRDS(T14_8_gfblup_variances_all,"T14_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_1_gblup_prediction_all_1_1000=readRDS(file="T15_1_gblup_prediction_all_1_1000.rds")
+T15_1_gblup_prediction_all_1001_2000=readRDS(file="T15_1_gblup_prediction_all_1001_2000.rds")
+T15_1_gblup_prediction_all_2001_3000=readRDS(file="T15_1_gblup_prediction_all_2001_3000.rds")
+T15_1_gblup_prediction_all_3001_4000=readRDS(file="T15_1_gblup_prediction_all_3001_4000.rds")
+T15_1_gblup_prediction_all_4001_5000=readRDS(file="T15_1_gblup_prediction_all_4001_5000.rds")
+T15_1_gblup_prediction_all_5001_6000=readRDS(file="T15_1_gblup_prediction_all_5001_6000.rds")
+T15_1_gblup_prediction_all_6001_7297=readRDS(file="T15_1_gblup_prediction_all_6001_7297.rds")
+T15_1_gblup_prediction_all=c(T15_1_gblup_prediction_all_1_1000,T15_1_gblup_prediction_all_1001_2000,T15_1_gblup_prediction_all_2001_3000,T15_1_gblup_prediction_all_3001_4000,T15_1_gblup_prediction_all_4001_5000,T15_1_gblup_prediction_all_5001_6000,T15_1_gblup_prediction_all_6001_7297)
+
+T15_1_gblup_variances_all_1_1000=readRDS(file="T15_1_gblup_variances_all_1_1000.rds")
+T15_1_gblup_variances_all_1001_2000=readRDS(file="T15_1_gblup_variances_all_1001_2000.rds")
+T15_1_gblup_variances_all_2001_3000=readRDS(file="T15_1_gblup_variances_all_2001_3000.rds")
+T15_1_gblup_variances_all_3001_4000=readRDS(file="T15_1_gblup_variances_all_3001_4000.rds")
+T15_1_gblup_variances_all_4001_5000=readRDS(file="T15_1_gblup_variances_all_4001_5000.rds")
+T15_1_gblup_variances_all_5001_6000=readRDS(file="T15_1_gblup_variances_all_5001_6000.rds")
+T15_1_gblup_variances_all_6001_7297=readRDS(file="T15_1_gblup_variances_all_6001_7297.rds")
+T15_1_gblup_variances_all=c(T15_1_gblup_variances_all_1_1000,T15_1_gblup_variances_all_1001_2000,T15_1_gblup_variances_all_2001_3000,T15_1_gblup_variances_all_3001_4000,T15_1_gblup_variances_all_4001_5000,T15_1_gblup_variances_all_5001_6000,T15_1_gblup_variances_all_6001_7297)
+
+saveRDS(T15_1_gblup_prediction_all,"T15_1_gblup_prediction_all.rds")
+saveRDS(T15_1_gblup_variances_all,"T15_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_1_gfblup_prediction_all_1_1000=readRDS(file="T15_1_gfblup_prediction_all_1_1000.rds")
+T15_1_gfblup_prediction_all_1001_2000=readRDS(file="T15_1_gfblup_prediction_all_1001_2000.rds")
+T15_1_gfblup_prediction_all_2001_3000=readRDS(file="T15_1_gfblup_prediction_all_2001_3000.rds")
+T15_1_gfblup_prediction_all_3001_4000=readRDS(file="T15_1_gfblup_prediction_all_3001_4000.rds")
+T15_1_gfblup_prediction_all_4001_5000=readRDS(file="T15_1_gfblup_prediction_all_4001_5000.rds")
+T15_1_gfblup_prediction_all_5001_6000=readRDS(file="T15_1_gfblup_prediction_all_5001_6000.rds")
+T15_1_gfblup_prediction_all_6001_7297=readRDS(file="T15_1_gfblup_prediction_all_6001_7297.rds")
+
+T15_1_gfblup_variances_all_1_1000=readRDS(file="T15_1_gfblup_variances_all_1_1000.rds")
+T15_1_gfblup_variances_all_1001_2000=readRDS(file="T15_1_gfblup_variances_all_1001_2000.rds")
+T15_1_gfblup_variances_all_2001_3000=readRDS(file="T15_1_gfblup_variances_all_2001_3000.rds")
+T15_1_gfblup_variances_all_3001_4000=readRDS(file="T15_1_gfblup_variances_all_3001_4000.rds")
+T15_1_gfblup_variances_all_4001_5000=readRDS(file="T15_1_gfblup_variances_all_4001_5000.rds")
+T15_1_gfblup_variances_all_5001_6000=readRDS(file="T15_1_gfblup_variances_all_5001_6000.rds")
+T15_1_gfblup_variances_all_6001_7297=readRDS(file="T15_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T15_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_1_gfblup_variances_all=rep(list(list()),cycles)
+T15_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_1_1000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_1001_2000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_2001_3000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_3001_4000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_4001_5000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_5001_6000[[r]])
+	T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_6001_7297[[r]])
+
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_1_1000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_1001_2000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_2001_3000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_3001_4000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_4001_5000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_5001_6000[[r]])
+	T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T15_1_gfblup_prediction_all,"T15_1_gfblup_prediction_all.rds")
+saveRDS(T15_1_gfblup_variances_all,"T15_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_2_gblup_prediction_all_1_1000=readRDS(file="T15_2_gblup_prediction_all_1_1000.rds")
+T15_2_gblup_prediction_all_1001_2000=readRDS(file="T15_2_gblup_prediction_all_1001_2000.rds")
+T15_2_gblup_prediction_all_2001_3000=readRDS(file="T15_2_gblup_prediction_all_2001_3000.rds")
+T15_2_gblup_prediction_all_3001_4000=readRDS(file="T15_2_gblup_prediction_all_3001_4000.rds")
+T15_2_gblup_prediction_all_4001_5000=readRDS(file="T15_2_gblup_prediction_all_4001_5000.rds")
+T15_2_gblup_prediction_all_5001_6000=readRDS(file="T15_2_gblup_prediction_all_5001_6000.rds")
+T15_2_gblup_prediction_all_6001_7297=readRDS(file="T15_2_gblup_prediction_all_6001_7297.rds")
+T15_2_gblup_prediction_all=c(T15_2_gblup_prediction_all_1_1000,T15_2_gblup_prediction_all_1001_2000,T15_2_gblup_prediction_all_2001_3000,T15_2_gblup_prediction_all_3001_4000,T15_2_gblup_prediction_all_4001_5000,T15_2_gblup_prediction_all_5001_6000,T15_2_gblup_prediction_all_6001_7297)
+
+T15_2_gblup_variances_all_1_1000=readRDS(file="T15_2_gblup_variances_all_1_1000.rds")
+T15_2_gblup_variances_all_1001_2000=readRDS(file="T15_2_gblup_variances_all_1001_2000.rds")
+T15_2_gblup_variances_all_2001_3000=readRDS(file="T15_2_gblup_variances_all_2001_3000.rds")
+T15_2_gblup_variances_all_3001_4000=readRDS(file="T15_2_gblup_variances_all_3001_4000.rds")
+T15_2_gblup_variances_all_4001_5000=readRDS(file="T15_2_gblup_variances_all_4001_5000.rds")
+T15_2_gblup_variances_all_5001_6000=readRDS(file="T15_2_gblup_variances_all_5001_6000.rds")
+T15_2_gblup_variances_all_6001_7297=readRDS(file="T15_2_gblup_variances_all_6001_7297.rds")
+T15_2_gblup_variances_all=c(T15_2_gblup_variances_all_1_1000,T15_2_gblup_variances_all_1001_2000,T15_2_gblup_variances_all_2001_3000,T15_2_gblup_variances_all_3001_4000,T15_2_gblup_variances_all_4001_5000,T15_2_gblup_variances_all_5001_6000,T15_2_gblup_variances_all_6001_7297)
+
+saveRDS(T15_2_gblup_prediction_all,"T15_2_gblup_prediction_all.rds")
+saveRDS(T15_2_gblup_variances_all,"T15_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_2_gfblup_prediction_all_1_1000=readRDS(file="T15_2_gfblup_prediction_all_1_1000.rds")
+T15_2_gfblup_prediction_all_1001_2000=readRDS(file="T15_2_gfblup_prediction_all_1001_2000.rds")
+T15_2_gfblup_prediction_all_2001_3000=readRDS(file="T15_2_gfblup_prediction_all_2001_3000.rds")
+T15_2_gfblup_prediction_all_3001_4000=readRDS(file="T15_2_gfblup_prediction_all_3001_4000.rds")
+T15_2_gfblup_prediction_all_4001_5000=readRDS(file="T15_2_gfblup_prediction_all_4001_5000.rds")
+T15_2_gfblup_prediction_all_5001_6000=readRDS(file="T15_2_gfblup_prediction_all_5001_6000.rds")
+T15_2_gfblup_prediction_all_6001_7297=readRDS(file="T15_2_gfblup_prediction_all_6001_7297.rds")
+
+T15_2_gfblup_variances_all_1_1000=readRDS(file="T15_2_gfblup_variances_all_1_1000.rds")
+T15_2_gfblup_variances_all_1001_2000=readRDS(file="T15_2_gfblup_variances_all_1001_2000.rds")
+T15_2_gfblup_variances_all_2001_3000=readRDS(file="T15_2_gfblup_variances_all_2001_3000.rds")
+T15_2_gfblup_variances_all_3001_4000=readRDS(file="T15_2_gfblup_variances_all_3001_4000.rds")
+T15_2_gfblup_variances_all_4001_5000=readRDS(file="T15_2_gfblup_variances_all_4001_5000.rds")
+T15_2_gfblup_variances_all_5001_6000=readRDS(file="T15_2_gfblup_variances_all_5001_6000.rds")
+T15_2_gfblup_variances_all_6001_7297=readRDS(file="T15_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T15_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_2_gfblup_variances_all=rep(list(list()),cycles)
+T15_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_1_1000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_1001_2000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_2001_3000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_3001_4000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_4001_5000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_5001_6000[[r]])
+	T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_6001_7297[[r]])
+
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_1_1000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_1001_2000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_2001_3000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_3001_4000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_4001_5000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_5001_6000[[r]])
+	T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T15_2_gfblup_prediction_all,"T15_2_gfblup_prediction_all.rds")
+saveRDS(T15_2_gfblup_variances_all,"T15_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_3_gblup_prediction_all_1_1000=readRDS(file="T15_3_gblup_prediction_all_1_1000.rds")
+T15_3_gblup_prediction_all_1001_2000=readRDS(file="T15_3_gblup_prediction_all_1001_2000.rds")
+T15_3_gblup_prediction_all_2001_3000=readRDS(file="T15_3_gblup_prediction_all_2001_3000.rds")
+T15_3_gblup_prediction_all_3001_4000=readRDS(file="T15_3_gblup_prediction_all_3001_4000.rds")
+T15_3_gblup_prediction_all_4001_5000=readRDS(file="T15_3_gblup_prediction_all_4001_5000.rds")
+T15_3_gblup_prediction_all_5001_6000=readRDS(file="T15_3_gblup_prediction_all_5001_6000.rds")
+T15_3_gblup_prediction_all_6001_7297=readRDS(file="T15_3_gblup_prediction_all_6001_7297.rds")
+T15_3_gblup_prediction_all=c(T15_3_gblup_prediction_all_1_1000,T15_3_gblup_prediction_all_1001_2000,T15_3_gblup_prediction_all_2001_3000,T15_3_gblup_prediction_all_3001_4000,T15_3_gblup_prediction_all_4001_5000,T15_3_gblup_prediction_all_5001_6000,T15_3_gblup_prediction_all_6001_7297)
+
+T15_3_gblup_variances_all_1_1000=readRDS(file="T15_3_gblup_variances_all_1_1000.rds")
+T15_3_gblup_variances_all_1001_2000=readRDS(file="T15_3_gblup_variances_all_1001_2000.rds")
+T15_3_gblup_variances_all_2001_3000=readRDS(file="T15_3_gblup_variances_all_2001_3000.rds")
+T15_3_gblup_variances_all_3001_4000=readRDS(file="T15_3_gblup_variances_all_3001_4000.rds")
+T15_3_gblup_variances_all_4001_5000=readRDS(file="T15_3_gblup_variances_all_4001_5000.rds")
+T15_3_gblup_variances_all_5001_6000=readRDS(file="T15_3_gblup_variances_all_5001_6000.rds")
+T15_3_gblup_variances_all_6001_7297=readRDS(file="T15_3_gblup_variances_all_6001_7297.rds")
+T15_3_gblup_variances_all=c(T15_3_gblup_variances_all_1_1000,T15_3_gblup_variances_all_1001_2000,T15_3_gblup_variances_all_2001_3000,T15_3_gblup_variances_all_3001_4000,T15_3_gblup_variances_all_4001_5000,T15_3_gblup_variances_all_5001_6000,T15_3_gblup_variances_all_6001_7297)
+
+saveRDS(T15_3_gblup_prediction_all,"T15_3_gblup_prediction_all.rds")
+saveRDS(T15_3_gblup_variances_all,"T15_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_3_gfblup_prediction_all_1_1000=readRDS(file="T15_3_gfblup_prediction_all_1_1000.rds")
+T15_3_gfblup_prediction_all_1001_2000=readRDS(file="T15_3_gfblup_prediction_all_1001_2000.rds")
+T15_3_gfblup_prediction_all_2001_3000=readRDS(file="T15_3_gfblup_prediction_all_2001_3000.rds")
+T15_3_gfblup_prediction_all_3001_4000=readRDS(file="T15_3_gfblup_prediction_all_3001_4000.rds")
+T15_3_gfblup_prediction_all_4001_5000=readRDS(file="T15_3_gfblup_prediction_all_4001_5000.rds")
+T15_3_gfblup_prediction_all_5001_6000=readRDS(file="T15_3_gfblup_prediction_all_5001_6000.rds")
+T15_3_gfblup_prediction_all_6001_7297=readRDS(file="T15_3_gfblup_prediction_all_6001_7297.rds")
+
+T15_3_gfblup_variances_all_1_1000=readRDS(file="T15_3_gfblup_variances_all_1_1000.rds")
+T15_3_gfblup_variances_all_1001_2000=readRDS(file="T15_3_gfblup_variances_all_1001_2000.rds")
+T15_3_gfblup_variances_all_2001_3000=readRDS(file="T15_3_gfblup_variances_all_2001_3000.rds")
+T15_3_gfblup_variances_all_3001_4000=readRDS(file="T15_3_gfblup_variances_all_3001_4000.rds")
+T15_3_gfblup_variances_all_4001_5000=readRDS(file="T15_3_gfblup_variances_all_4001_5000.rds")
+T15_3_gfblup_variances_all_5001_6000=readRDS(file="T15_3_gfblup_variances_all_5001_6000.rds")
+T15_3_gfblup_variances_all_6001_7297=readRDS(file="T15_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T15_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_3_gfblup_variances_all=rep(list(list()),cycles)
+T15_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_1_1000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_1001_2000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_2001_3000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_3001_4000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_4001_5000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_5001_6000[[r]])
+	T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_6001_7297[[r]])
+
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_1_1000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_1001_2000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_2001_3000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_3001_4000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_4001_5000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_5001_6000[[r]])
+	T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T15_3_gfblup_prediction_all,"T15_3_gfblup_prediction_all.rds")
+saveRDS(T15_3_gfblup_variances_all,"T15_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_4_gblup_prediction_all_1_1000=readRDS(file="T15_4_gblup_prediction_all_1_1000.rds")
+T15_4_gblup_prediction_all_1001_2000=readRDS(file="T15_4_gblup_prediction_all_1001_2000.rds")
+T15_4_gblup_prediction_all_2001_3000=readRDS(file="T15_4_gblup_prediction_all_2001_3000.rds")
+T15_4_gblup_prediction_all_3001_4000=readRDS(file="T15_4_gblup_prediction_all_3001_4000.rds")
+T15_4_gblup_prediction_all_4001_5000=readRDS(file="T15_4_gblup_prediction_all_4001_5000.rds")
+T15_4_gblup_prediction_all_5001_6000=readRDS(file="T15_4_gblup_prediction_all_5001_6000.rds")
+T15_4_gblup_prediction_all_6001_7297=readRDS(file="T15_4_gblup_prediction_all_6001_7297.rds")
+T15_4_gblup_prediction_all=c(T15_4_gblup_prediction_all_1_1000,T15_4_gblup_prediction_all_1001_2000,T15_4_gblup_prediction_all_2001_3000,T15_4_gblup_prediction_all_3001_4000,T15_4_gblup_prediction_all_4001_5000,T15_4_gblup_prediction_all_5001_6000,T15_4_gblup_prediction_all_6001_7297)
+
+T15_4_gblup_variances_all_1_1000=readRDS(file="T15_4_gblup_variances_all_1_1000.rds")
+T15_4_gblup_variances_all_1001_2000=readRDS(file="T15_4_gblup_variances_all_1001_2000.rds")
+T15_4_gblup_variances_all_2001_3000=readRDS(file="T15_4_gblup_variances_all_2001_3000.rds")
+T15_4_gblup_variances_all_3001_4000=readRDS(file="T15_4_gblup_variances_all_3001_4000.rds")
+T15_4_gblup_variances_all_4001_5000=readRDS(file="T15_4_gblup_variances_all_4001_5000.rds")
+T15_4_gblup_variances_all_5001_6000=readRDS(file="T15_4_gblup_variances_all_5001_6000.rds")
+T15_4_gblup_variances_all_6001_7297=readRDS(file="T15_4_gblup_variances_all_6001_7297.rds")
+T15_4_gblup_variances_all=c(T15_4_gblup_variances_all_1_1000,T15_4_gblup_variances_all_1001_2000,T15_4_gblup_variances_all_2001_3000,T15_4_gblup_variances_all_3001_4000,T15_4_gblup_variances_all_4001_5000,T15_4_gblup_variances_all_5001_6000,T15_4_gblup_variances_all_6001_7297)
+
+saveRDS(T15_4_gblup_prediction_all,"T15_4_gblup_prediction_all.rds")
+saveRDS(T15_4_gblup_variances_all,"T15_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_4_gfblup_prediction_all_1_1000=readRDS(file="T15_4_gfblup_prediction_all_1_1000.rds")
+T15_4_gfblup_prediction_all_1001_2000=readRDS(file="T15_4_gfblup_prediction_all_1001_2000.rds")
+T15_4_gfblup_prediction_all_2001_3000=readRDS(file="T15_4_gfblup_prediction_all_2001_3000.rds")
+T15_4_gfblup_prediction_all_3001_4000=readRDS(file="T15_4_gfblup_prediction_all_3001_4000.rds")
+T15_4_gfblup_prediction_all_4001_5000=readRDS(file="T15_4_gfblup_prediction_all_4001_5000.rds")
+T15_4_gfblup_prediction_all_5001_6000=readRDS(file="T15_4_gfblup_prediction_all_5001_6000.rds")
+T15_4_gfblup_prediction_all_6001_7297=readRDS(file="T15_4_gfblup_prediction_all_6001_7297.rds")
+
+T15_4_gfblup_variances_all_1_1000=readRDS(file="T15_4_gfblup_variances_all_1_1000.rds")
+T15_4_gfblup_variances_all_1001_2000=readRDS(file="T15_4_gfblup_variances_all_1001_2000.rds")
+T15_4_gfblup_variances_all_2001_3000=readRDS(file="T15_4_gfblup_variances_all_2001_3000.rds")
+T15_4_gfblup_variances_all_3001_4000=readRDS(file="T15_4_gfblup_variances_all_3001_4000.rds")
+T15_4_gfblup_variances_all_4001_5000=readRDS(file="T15_4_gfblup_variances_all_4001_5000.rds")
+T15_4_gfblup_variances_all_5001_6000=readRDS(file="T15_4_gfblup_variances_all_5001_6000.rds")
+T15_4_gfblup_variances_all_6001_7297=readRDS(file="T15_4_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T15_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_4_gfblup_variances_all=rep(list(list()),cycles)
+T15_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_1_1000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_1001_2000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_2001_3000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_3001_4000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_4001_5000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_5001_6000[[r]])
+	T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_6001_7297[[r]])
+
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_1_1000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_1001_2000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_2001_3000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_3001_4000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_4001_5000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_5001_6000[[r]])
+	T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T15_4_gfblup_prediction_all,"T15_4_gfblup_prediction_all.rds")
+saveRDS(T15_4_gfblup_variances_all,"T15_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_5_gblup_prediction_all_1_1000=readRDS(file="T15_5_gblup_prediction_all_1_1000.rds")
+T15_5_gblup_prediction_all_1001_2000=readRDS(file="T15_5_gblup_prediction_all_1001_2000.rds")
+T15_5_gblup_prediction_all_2001_3000=readRDS(file="T15_5_gblup_prediction_all_2001_3000.rds")
+T15_5_gblup_prediction_all_3001_4000=readRDS(file="T15_5_gblup_prediction_all_3001_4000.rds")
+T15_5_gblup_prediction_all_4001_5000=readRDS(file="T15_5_gblup_prediction_all_4001_5000.rds")
+T15_5_gblup_prediction_all_5001_6000=readRDS(file="T15_5_gblup_prediction_all_5001_6000.rds")
+T15_5_gblup_prediction_all_6001_7297=readRDS(file="T15_5_gblup_prediction_all_6001_7297.rds")
+T15_5_gblup_prediction_all=c(T15_5_gblup_prediction_all_1_1000,T15_5_gblup_prediction_all_1001_2000,T15_5_gblup_prediction_all_2001_3000,T15_5_gblup_prediction_all_3001_4000,T15_5_gblup_prediction_all_4001_5000,T15_5_gblup_prediction_all_5001_6000,T15_5_gblup_prediction_all_6001_7297)
+
+T15_5_gblup_variances_all_1_1000=readRDS(file="T15_5_gblup_variances_all_1_1000.rds")
+T15_5_gblup_variances_all_1001_2000=readRDS(file="T15_5_gblup_variances_all_1001_2000.rds")
+T15_5_gblup_variances_all_2001_3000=readRDS(file="T15_5_gblup_variances_all_2001_3000.rds")
+T15_5_gblup_variances_all_3001_4000=readRDS(file="T15_5_gblup_variances_all_3001_4000.rds")
+T15_5_gblup_variances_all_4001_5000=readRDS(file="T15_5_gblup_variances_all_4001_5000.rds")
+T15_5_gblup_variances_all_5001_6000=readRDS(file="T15_5_gblup_variances_all_5001_6000.rds")
+T15_5_gblup_variances_all_6001_7297=readRDS(file="T15_5_gblup_variances_all_6001_7297.rds")
+T15_5_gblup_variances_all=c(T15_5_gblup_variances_all_1_1000,T15_5_gblup_variances_all_1001_2000,T15_5_gblup_variances_all_2001_3000,T15_5_gblup_variances_all_3001_4000,T15_5_gblup_variances_all_4001_5000,T15_5_gblup_variances_all_5001_6000,T15_5_gblup_variances_all_6001_7297)
+
+saveRDS(T15_5_gblup_prediction_all,"T15_5_gblup_prediction_all.rds")
+saveRDS(T15_5_gblup_variances_all,"T15_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_5_gfblup_prediction_all_1_1000=readRDS(file="T15_5_gfblup_prediction_all_1_1000.rds")
+T15_5_gfblup_prediction_all_1001_2000=readRDS(file="T15_5_gfblup_prediction_all_1001_2000.rds")
+T15_5_gfblup_prediction_all_2001_3000=readRDS(file="T15_5_gfblup_prediction_all_2001_3000.rds")
+T15_5_gfblup_prediction_all_3001_4000=readRDS(file="T15_5_gfblup_prediction_all_3001_4000.rds")
+T15_5_gfblup_prediction_all_4001_5000=readRDS(file="T15_5_gfblup_prediction_all_4001_5000.rds")
+T15_5_gfblup_prediction_all_5001_6000=readRDS(file="T15_5_gfblup_prediction_all_5001_6000.rds")
+T15_5_gfblup_prediction_all_6001_7297=readRDS(file="T15_5_gfblup_prediction_all_6001_7297.rds")
+
+T15_5_gfblup_variances_all_1_1000=readRDS(file="T15_5_gfblup_variances_all_1_1000.rds")
+T15_5_gfblup_variances_all_1001_2000=readRDS(file="T15_5_gfblup_variances_all_1001_2000.rds")
+T15_5_gfblup_variances_all_2001_3000=readRDS(file="T15_5_gfblup_variances_all_2001_3000.rds")
+T15_5_gfblup_variances_all_3001_4000=readRDS(file="T15_5_gfblup_variances_all_3001_4000.rds")
+T15_5_gfblup_variances_all_4001_5000=readRDS(file="T15_5_gfblup_variances_all_4001_5000.rds")
+T15_5_gfblup_variances_all_5001_6000=readRDS(file="T15_5_gfblup_variances_all_5001_6000.rds")
+T15_5_gfblup_variances_all_6001_7297=readRDS(file="T15_5_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T15_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_5_gfblup_variances_all=rep(list(list()),cycles)
+T15_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_1_1000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_1001_2000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_2001_3000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_3001_4000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_4001_5000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_5001_6000[[r]])
+	T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_6001_7297[[r]])
+
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_1_1000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_1001_2000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_2001_3000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_3001_4000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_4001_5000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_5001_6000[[r]])
+	T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T15_5_gfblup_prediction_all,"T15_5_gfblup_prediction_all.rds")
+saveRDS(T15_5_gfblup_variances_all,"T15_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_6_gblup_prediction_all_1_1000=readRDS(file="T15_6_gblup_prediction_all_1_1000.rds")
+T15_6_gblup_prediction_all_1001_2000=readRDS(file="T15_6_gblup_prediction_all_1001_2000.rds")
+T15_6_gblup_prediction_all_2001_3000=readRDS(file="T15_6_gblup_prediction_all_2001_3000.rds")
+T15_6_gblup_prediction_all_3001_4000=readRDS(file="T15_6_gblup_prediction_all_3001_4000.rds")
+T15_6_gblup_prediction_all_4001_5000=readRDS(file="T15_6_gblup_prediction_all_4001_5000.rds")
+T15_6_gblup_prediction_all_5001_6000=readRDS(file="T15_6_gblup_prediction_all_5001_6000.rds")
+T15_6_gblup_prediction_all_6001_7297=readRDS(file="T15_6_gblup_prediction_all_6001_7297.rds")
+T15_6_gblup_prediction_all=c(T15_6_gblup_prediction_all_1_1000,T15_6_gblup_prediction_all_1001_2000,T15_6_gblup_prediction_all_2001_3000,T15_6_gblup_prediction_all_3001_4000,T15_6_gblup_prediction_all_4001_5000,T15_6_gblup_prediction_all_5001_6000,T15_6_gblup_prediction_all_6001_7297)
+
+T15_6_gblup_variances_all_1_1000=readRDS(file="T15_6_gblup_variances_all_1_1000.rds")
+T15_6_gblup_variances_all_1001_2000=readRDS(file="T15_6_gblup_variances_all_1001_2000.rds")
+T15_6_gblup_variances_all_2001_3000=readRDS(file="T15_6_gblup_variances_all_2001_3000.rds")
+T15_6_gblup_variances_all_3001_4000=readRDS(file="T15_6_gblup_variances_all_3001_4000.rds")
+T15_6_gblup_variances_all_4001_5000=readRDS(file="T15_6_gblup_variances_all_4001_5000.rds")
+T15_6_gblup_variances_all_5001_6000=readRDS(file="T15_6_gblup_variances_all_5001_6000.rds")
+T15_6_gblup_variances_all_6001_7297=readRDS(file="T15_6_gblup_variances_all_6001_7297.rds")
+T15_6_gblup_variances_all=c(T15_6_gblup_variances_all_1_1000,T15_6_gblup_variances_all_1001_2000,T15_6_gblup_variances_all_2001_3000,T15_6_gblup_variances_all_3001_4000,T15_6_gblup_variances_all_4001_5000,T15_6_gblup_variances_all_5001_6000,T15_6_gblup_variances_all_6001_7297)
+
+saveRDS(T15_6_gblup_prediction_all,"T15_6_gblup_prediction_all.rds")
+saveRDS(T15_6_gblup_variances_all,"T15_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_6_gfblup_prediction_all_1_1000=readRDS(file="T15_6_gfblup_prediction_all_1_1000.rds")
+T15_6_gfblup_prediction_all_1001_2000=readRDS(file="T15_6_gfblup_prediction_all_1001_2000.rds")
+T15_6_gfblup_prediction_all_2001_3000=readRDS(file="T15_6_gfblup_prediction_all_2001_3000.rds")
+T15_6_gfblup_prediction_all_3001_4000=readRDS(file="T15_6_gfblup_prediction_all_3001_4000.rds")
+T15_6_gfblup_prediction_all_4001_5000=readRDS(file="T15_6_gfblup_prediction_all_4001_5000.rds")
+T15_6_gfblup_prediction_all_5001_6000=readRDS(file="T15_6_gfblup_prediction_all_5001_6000.rds")
+T15_6_gfblup_prediction_all_6001_7297=readRDS(file="T15_6_gfblup_prediction_all_6001_7297.rds")
+
+T15_6_gfblup_variances_all_1_1000=readRDS(file="T15_6_gfblup_variances_all_1_1000.rds")
+T15_6_gfblup_variances_all_1001_2000=readRDS(file="T15_6_gfblup_variances_all_1001_2000.rds")
+T15_6_gfblup_variances_all_2001_3000=readRDS(file="T15_6_gfblup_variances_all_2001_3000.rds")
+T15_6_gfblup_variances_all_3001_4000=readRDS(file="T15_6_gfblup_variances_all_3001_4000.rds")
+T15_6_gfblup_variances_all_4001_5000=readRDS(file="T15_6_gfblup_variances_all_4001_5000.rds")
+T15_6_gfblup_variances_all_5001_6000=readRDS(file="T15_6_gfblup_variances_all_5001_6000.rds")
+T15_6_gfblup_variances_all_6001_7297=readRDS(file="T15_6_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T15_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_6_gfblup_variances_all=rep(list(list()),cycles)
+T15_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_1_1000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_1001_2000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_2001_3000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_3001_4000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_4001_5000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_5001_6000[[r]])
+	T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_6001_7297[[r]])
+
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_1_1000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_1001_2000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_2001_3000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_3001_4000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_4001_5000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_5001_6000[[r]])
+	T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T15_6_gfblup_prediction_all,"T15_6_gfblup_prediction_all.rds")
+saveRDS(T15_6_gfblup_variances_all,"T15_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_7_gblup_prediction_all_1_1000=readRDS(file="T15_7_gblup_prediction_all_1_1000.rds")
+T15_7_gblup_prediction_all_1001_2000=readRDS(file="T15_7_gblup_prediction_all_1001_2000.rds")
+T15_7_gblup_prediction_all_2001_3000=readRDS(file="T15_7_gblup_prediction_all_2001_3000.rds")
+T15_7_gblup_prediction_all_3001_4000=readRDS(file="T15_7_gblup_prediction_all_3001_4000.rds")
+T15_7_gblup_prediction_all_4001_5000=readRDS(file="T15_7_gblup_prediction_all_4001_5000.rds")
+T15_7_gblup_prediction_all_5001_6000=readRDS(file="T15_7_gblup_prediction_all_5001_6000.rds")
+T15_7_gblup_prediction_all_6001_7297=readRDS(file="T15_7_gblup_prediction_all_6001_7297.rds")
+T15_7_gblup_prediction_all=c(T15_7_gblup_prediction_all_1_1000,T15_7_gblup_prediction_all_1001_2000,T15_7_gblup_prediction_all_2001_3000,T15_7_gblup_prediction_all_3001_4000,T15_7_gblup_prediction_all_4001_5000,T15_7_gblup_prediction_all_5001_6000,T15_7_gblup_prediction_all_6001_7297)
+
+T15_7_gblup_variances_all_1_1000=readRDS(file="T15_7_gblup_variances_all_1_1000.rds")
+T15_7_gblup_variances_all_1001_2000=readRDS(file="T15_7_gblup_variances_all_1001_2000.rds")
+T15_7_gblup_variances_all_2001_3000=readRDS(file="T15_7_gblup_variances_all_2001_3000.rds")
+T15_7_gblup_variances_all_3001_4000=readRDS(file="T15_7_gblup_variances_all_3001_4000.rds")
+T15_7_gblup_variances_all_4001_5000=readRDS(file="T15_7_gblup_variances_all_4001_5000.rds")
+T15_7_gblup_variances_all_5001_6000=readRDS(file="T15_7_gblup_variances_all_5001_6000.rds")
+T15_7_gblup_variances_all_6001_7297=readRDS(file="T15_7_gblup_variances_all_6001_7297.rds")
+T15_7_gblup_variances_all=c(T15_7_gblup_variances_all_1_1000,T15_7_gblup_variances_all_1001_2000,T15_7_gblup_variances_all_2001_3000,T15_7_gblup_variances_all_3001_4000,T15_7_gblup_variances_all_4001_5000,T15_7_gblup_variances_all_5001_6000,T15_7_gblup_variances_all_6001_7297)
+
+saveRDS(T15_7_gblup_prediction_all,"T15_7_gblup_prediction_all.rds")
+saveRDS(T15_7_gblup_variances_all,"T15_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_7_gfblup_prediction_all_1_1000=readRDS(file="T15_7_gfblup_prediction_all_1_1000.rds")
+T15_7_gfblup_prediction_all_1001_2000=readRDS(file="T15_7_gfblup_prediction_all_1001_2000.rds")
+T15_7_gfblup_prediction_all_2001_3000=readRDS(file="T15_7_gfblup_prediction_all_2001_3000.rds")
+T15_7_gfblup_prediction_all_3001_4000=readRDS(file="T15_7_gfblup_prediction_all_3001_4000.rds")
+T15_7_gfblup_prediction_all_4001_5000=readRDS(file="T15_7_gfblup_prediction_all_4001_5000.rds")
+T15_7_gfblup_prediction_all_5001_6000=readRDS(file="T15_7_gfblup_prediction_all_5001_6000.rds")
+T15_7_gfblup_prediction_all_6001_7297=readRDS(file="T15_7_gfblup_prediction_all_6001_7297.rds")
+
+T15_7_gfblup_variances_all_1_1000=readRDS(file="T15_7_gfblup_variances_all_1_1000.rds")
+T15_7_gfblup_variances_all_1001_2000=readRDS(file="T15_7_gfblup_variances_all_1001_2000.rds")
+T15_7_gfblup_variances_all_2001_3000=readRDS(file="T15_7_gfblup_variances_all_2001_3000.rds")
+T15_7_gfblup_variances_all_3001_4000=readRDS(file="T15_7_gfblup_variances_all_3001_4000.rds")
+T15_7_gfblup_variances_all_4001_5000=readRDS(file="T15_7_gfblup_variances_all_4001_5000.rds")
+T15_7_gfblup_variances_all_5001_6000=readRDS(file="T15_7_gfblup_variances_all_5001_6000.rds")
+T15_7_gfblup_variances_all_6001_7297=readRDS(file="T15_7_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T15_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_7_gfblup_variances_all=rep(list(list()),cycles)
+T15_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_1_1000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_1001_2000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_2001_3000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_3001_4000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_4001_5000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_5001_6000[[r]])
+	T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_6001_7297[[r]])
+
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_1_1000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_1001_2000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_2001_3000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_3001_4000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_4001_5000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_5001_6000[[r]])
+	T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T15_7_gfblup_prediction_all,"T15_7_gfblup_prediction_all.rds")
+saveRDS(T15_7_gfblup_variances_all,"T15_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_8_gblup_prediction_all_1_1000=readRDS(file="T15_8_gblup_prediction_all_1_1000.rds")
+T15_8_gblup_prediction_all_1001_2000=readRDS(file="T15_8_gblup_prediction_all_1001_2000.rds")
+T15_8_gblup_prediction_all_2001_3000=readRDS(file="T15_8_gblup_prediction_all_2001_3000.rds")
+T15_8_gblup_prediction_all_3001_4000=readRDS(file="T15_8_gblup_prediction_all_3001_4000.rds")
+T15_8_gblup_prediction_all_4001_5000=readRDS(file="T15_8_gblup_prediction_all_4001_5000.rds")
+T15_8_gblup_prediction_all_5001_6000=readRDS(file="T15_8_gblup_prediction_all_5001_6000.rds")
+T15_8_gblup_prediction_all_6001_7297=readRDS(file="T15_8_gblup_prediction_all_6001_7297.rds")
+T15_8_gblup_prediction_all=c(T15_8_gblup_prediction_all_1_1000,T15_8_gblup_prediction_all_1001_2000,T15_8_gblup_prediction_all_2001_3000,T15_8_gblup_prediction_all_3001_4000,T15_8_gblup_prediction_all_4001_5000,T15_8_gblup_prediction_all_5001_6000,T15_8_gblup_prediction_all_6001_7297)
+
+T15_8_gblup_variances_all_1_1000=readRDS(file="T15_8_gblup_variances_all_1_1000.rds")
+T15_8_gblup_variances_all_1001_2000=readRDS(file="T15_8_gblup_variances_all_1001_2000.rds")
+T15_8_gblup_variances_all_2001_3000=readRDS(file="T15_8_gblup_variances_all_2001_3000.rds")
+T15_8_gblup_variances_all_3001_4000=readRDS(file="T15_8_gblup_variances_all_3001_4000.rds")
+T15_8_gblup_variances_all_4001_5000=readRDS(file="T15_8_gblup_variances_all_4001_5000.rds")
+T15_8_gblup_variances_all_5001_6000=readRDS(file="T15_8_gblup_variances_all_5001_6000.rds")
+T15_8_gblup_variances_all_6001_7297=readRDS(file="T15_8_gblup_variances_all_6001_7297.rds")
+T15_8_gblup_variances_all=c(T15_8_gblup_variances_all_1_1000,T15_8_gblup_variances_all_1001_2000,T15_8_gblup_variances_all_2001_3000,T15_8_gblup_variances_all_3001_4000,T15_8_gblup_variances_all_4001_5000,T15_8_gblup_variances_all_5001_6000,T15_8_gblup_variances_all_6001_7297)
+
+saveRDS(T15_8_gblup_prediction_all,"T15_8_gblup_prediction_all.rds")
+saveRDS(T15_8_gblup_variances_all,"T15_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T15_8_gfblup_prediction_all_1_1000=readRDS(file="T15_8_gfblup_prediction_all_1_1000.rds")
+T15_8_gfblup_prediction_all_1001_2000=readRDS(file="T15_8_gfblup_prediction_all_1001_2000.rds")
+T15_8_gfblup_prediction_all_2001_3000=readRDS(file="T15_8_gfblup_prediction_all_2001_3000.rds")
+T15_8_gfblup_prediction_all_3001_4000=readRDS(file="T15_8_gfblup_prediction_all_3001_4000.rds")
+T15_8_gfblup_prediction_all_4001_5000=readRDS(file="T15_8_gfblup_prediction_all_4001_5000.rds")
+T15_8_gfblup_prediction_all_5001_6000=readRDS(file="T15_8_gfblup_prediction_all_5001_6000.rds")
+T15_8_gfblup_prediction_all_6001_7297=readRDS(file="T15_8_gfblup_prediction_all_6001_7297.rds")
+
+T15_8_gfblup_variances_all_1_1000=readRDS(file="T15_8_gfblup_variances_all_1_1000.rds")
+T15_8_gfblup_variances_all_1001_2000=readRDS(file="T15_8_gfblup_variances_all_1001_2000.rds")
+T15_8_gfblup_variances_all_2001_3000=readRDS(file="T15_8_gfblup_variances_all_2001_3000.rds")
+T15_8_gfblup_variances_all_3001_4000=readRDS(file="T15_8_gfblup_variances_all_3001_4000.rds")
+T15_8_gfblup_variances_all_4001_5000=readRDS(file="T15_8_gfblup_variances_all_4001_5000.rds")
+T15_8_gfblup_variances_all_5001_6000=readRDS(file="T15_8_gfblup_variances_all_5001_6000.rds")
+T15_8_gfblup_variances_all_6001_7297=readRDS(file="T15_8_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T15_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T15_8_gfblup_variances_all=rep(list(list()),cycles)
+T15_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_1_1000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_1001_2000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_2001_3000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_3001_4000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_4001_5000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_5001_6000[[r]])
+	T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_6001_7297[[r]])
+
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_1_1000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_1001_2000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_2001_3000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_3001_4000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_4001_5000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_5001_6000[[r]])
+	T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T15_8_gfblup_prediction_all,"T15_8_gfblup_prediction_all.rds")
+saveRDS(T15_8_gfblup_variances_all,"T15_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_1_gblup_prediction_all_1_1000=readRDS(file="T16_1_gblup_prediction_all_1_1000.rds")
+T16_1_gblup_prediction_all_1001_2000=readRDS(file="T16_1_gblup_prediction_all_1001_2000.rds")
+T16_1_gblup_prediction_all_2001_3000=readRDS(file="T16_1_gblup_prediction_all_2001_3000.rds")
+T16_1_gblup_prediction_all_3001_4000=readRDS(file="T16_1_gblup_prediction_all_3001_4000.rds")
+T16_1_gblup_prediction_all_4001_5000=readRDS(file="T16_1_gblup_prediction_all_4001_5000.rds")
+T16_1_gblup_prediction_all_5001_6000=readRDS(file="T16_1_gblup_prediction_all_5001_6000.rds")
+T16_1_gblup_prediction_all_6001_7297=readRDS(file="T16_1_gblup_prediction_all_6001_7297.rds")
+T16_1_gblup_prediction_all=c(T16_1_gblup_prediction_all_1_1000,T16_1_gblup_prediction_all_1001_2000,T16_1_gblup_prediction_all_2001_3000,T16_1_gblup_prediction_all_3001_4000,T16_1_gblup_prediction_all_4001_5000,T16_1_gblup_prediction_all_5001_6000,T16_1_gblup_prediction_all_6001_7297)
+
+T16_1_gblup_variances_all_1_1000=readRDS(file="T16_1_gblup_variances_all_1_1000.rds")
+T16_1_gblup_variances_all_1001_2000=readRDS(file="T16_1_gblup_variances_all_1001_2000.rds")
+T16_1_gblup_variances_all_2001_3000=readRDS(file="T16_1_gblup_variances_all_2001_3000.rds")
+T16_1_gblup_variances_all_3001_4000=readRDS(file="T16_1_gblup_variances_all_3001_4000.rds")
+T16_1_gblup_variances_all_4001_5000=readRDS(file="T16_1_gblup_variances_all_4001_5000.rds")
+T16_1_gblup_variances_all_5001_6000=readRDS(file="T16_1_gblup_variances_all_5001_6000.rds")
+T16_1_gblup_variances_all_6001_7297=readRDS(file="T16_1_gblup_variances_all_6001_7297.rds")
+T16_1_gblup_variances_all=c(T16_1_gblup_variances_all_1_1000,T16_1_gblup_variances_all_1001_2000,T16_1_gblup_variances_all_2001_3000,T16_1_gblup_variances_all_3001_4000,T16_1_gblup_variances_all_4001_5000,T16_1_gblup_variances_all_5001_6000,T16_1_gblup_variances_all_6001_7297)
+
+saveRDS(T16_1_gblup_prediction_all,"T16_1_gblup_prediction_all.rds")
+saveRDS(T16_1_gblup_variances_all,"T16_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_1_gfblup_prediction_all_1_1000=readRDS(file="T16_1_gfblup_prediction_all_1_1000.rds")
+T16_1_gfblup_prediction_all_1001_2000=readRDS(file="T16_1_gfblup_prediction_all_1001_2000.rds")
+T16_1_gfblup_prediction_all_2001_3000=readRDS(file="T16_1_gfblup_prediction_all_2001_3000.rds")
+T16_1_gfblup_prediction_all_3001_4000=readRDS(file="T16_1_gfblup_prediction_all_3001_4000.rds")
+T16_1_gfblup_prediction_all_4001_5000=readRDS(file="T16_1_gfblup_prediction_all_4001_5000.rds")
+T16_1_gfblup_prediction_all_5001_6000=readRDS(file="T16_1_gfblup_prediction_all_5001_6000.rds")
+T16_1_gfblup_prediction_all_6001_7297=readRDS(file="T16_1_gfblup_prediction_all_6001_7297.rds")
+
+T16_1_gfblup_variances_all_1_1000=readRDS(file="T16_1_gfblup_variances_all_1_1000.rds")
+T16_1_gfblup_variances_all_1001_2000=readRDS(file="T16_1_gfblup_variances_all_1001_2000.rds")
+T16_1_gfblup_variances_all_2001_3000=readRDS(file="T16_1_gfblup_variances_all_2001_3000.rds")
+T16_1_gfblup_variances_all_3001_4000=readRDS(file="T16_1_gfblup_variances_all_3001_4000.rds")
+T16_1_gfblup_variances_all_4001_5000=readRDS(file="T16_1_gfblup_variances_all_4001_5000.rds")
+T16_1_gfblup_variances_all_5001_6000=readRDS(file="T16_1_gfblup_variances_all_5001_6000.rds")
+T16_1_gfblup_variances_all_6001_7297=readRDS(file="T16_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T16_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_1_gfblup_variances_all=rep(list(list()),cycles)
+T16_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_1_1000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_1001_2000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_2001_3000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_3001_4000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_4001_5000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_5001_6000[[r]])
+	T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_6001_7297[[r]])
+
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_1_1000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_1001_2000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_2001_3000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_3001_4000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_4001_5000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_5001_6000[[r]])
+	T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T16_1_gfblup_prediction_all,"T16_1_gfblup_prediction_all.rds")
+saveRDS(T16_1_gfblup_variances_all,"T16_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_2_gblup_prediction_all_1_1000=readRDS(file="T16_2_gblup_prediction_all_1_1000.rds")
+T16_2_gblup_prediction_all_1001_2000=readRDS(file="T16_2_gblup_prediction_all_1001_2000.rds")
+T16_2_gblup_prediction_all_2001_3000=readRDS(file="T16_2_gblup_prediction_all_2001_3000.rds")
+T16_2_gblup_prediction_all_3001_4000=readRDS(file="T16_2_gblup_prediction_all_3001_4000.rds")
+T16_2_gblup_prediction_all_4001_5000=readRDS(file="T16_2_gblup_prediction_all_4001_5000.rds")
+T16_2_gblup_prediction_all_5001_6000=readRDS(file="T16_2_gblup_prediction_all_5001_6000.rds")
+T16_2_gblup_prediction_all_6001_7297=readRDS(file="T16_2_gblup_prediction_all_6001_7297.rds")
+T16_2_gblup_prediction_all=c(T16_2_gblup_prediction_all_1_1000,T16_2_gblup_prediction_all_1001_2000,T16_2_gblup_prediction_all_2001_3000,T16_2_gblup_prediction_all_3001_4000,T16_2_gblup_prediction_all_4001_5000,T16_2_gblup_prediction_all_5001_6000,T16_2_gblup_prediction_all_6001_7297)
+
+T16_2_gblup_variances_all_1_1000=readRDS(file="T16_2_gblup_variances_all_1_1000.rds")
+T16_2_gblup_variances_all_1001_2000=readRDS(file="T16_2_gblup_variances_all_1001_2000.rds")
+T16_2_gblup_variances_all_2001_3000=readRDS(file="T16_2_gblup_variances_all_2001_3000.rds")
+T16_2_gblup_variances_all_3001_4000=readRDS(file="T16_2_gblup_variances_all_3001_4000.rds")
+T16_2_gblup_variances_all_4001_5000=readRDS(file="T16_2_gblup_variances_all_4001_5000.rds")
+T16_2_gblup_variances_all_5001_6000=readRDS(file="T16_2_gblup_variances_all_5001_6000.rds")
+T16_2_gblup_variances_all_6001_7297=readRDS(file="T16_2_gblup_variances_all_6001_7297.rds")
+T16_2_gblup_variances_all=c(T16_2_gblup_variances_all_1_1000,T16_2_gblup_variances_all_1001_2000,T16_2_gblup_variances_all_2001_3000,T16_2_gblup_variances_all_3001_4000,T16_2_gblup_variances_all_4001_5000,T16_2_gblup_variances_all_5001_6000,T16_2_gblup_variances_all_6001_7297)
+
+saveRDS(T16_2_gblup_prediction_all,"T16_2_gblup_prediction_all.rds")
+saveRDS(T16_2_gblup_variances_all,"T16_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_2_gfblup_prediction_all_1_1000=readRDS(file="T16_2_gfblup_prediction_all_1_1000.rds")
+T16_2_gfblup_prediction_all_1001_2000=readRDS(file="T16_2_gfblup_prediction_all_1001_2000.rds")
+T16_2_gfblup_prediction_all_2001_3000=readRDS(file="T16_2_gfblup_prediction_all_2001_3000.rds")
+T16_2_gfblup_prediction_all_3001_4000=readRDS(file="T16_2_gfblup_prediction_all_3001_4000.rds")
+T16_2_gfblup_prediction_all_4001_5000=readRDS(file="T16_2_gfblup_prediction_all_4001_5000.rds")
+T16_2_gfblup_prediction_all_5001_6000=readRDS(file="T16_2_gfblup_prediction_all_5001_6000.rds")
+T16_2_gfblup_prediction_all_6001_7297=readRDS(file="T16_2_gfblup_prediction_all_6001_7297.rds")
+
+T16_2_gfblup_variances_all_1_1000=readRDS(file="T16_2_gfblup_variances_all_1_1000.rds")
+T16_2_gfblup_variances_all_1001_2000=readRDS(file="T16_2_gfblup_variances_all_1001_2000.rds")
+T16_2_gfblup_variances_all_2001_3000=readRDS(file="T16_2_gfblup_variances_all_2001_3000.rds")
+T16_2_gfblup_variances_all_3001_4000=readRDS(file="T16_2_gfblup_variances_all_3001_4000.rds")
+T16_2_gfblup_variances_all_4001_5000=readRDS(file="T16_2_gfblup_variances_all_4001_5000.rds")
+T16_2_gfblup_variances_all_5001_6000=readRDS(file="T16_2_gfblup_variances_all_5001_6000.rds")
+T16_2_gfblup_variances_all_6001_7297=readRDS(file="T16_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T16_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_2_gfblup_variances_all=rep(list(list()),cycles)
+T16_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_1_1000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_1001_2000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_2001_3000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_3001_4000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_4001_5000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_5001_6000[[r]])
+	T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_6001_7297[[r]])
+
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_1_1000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_1001_2000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_2001_3000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_3001_4000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_4001_5000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_5001_6000[[r]])
+	T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T16_2_gfblup_prediction_all,"T16_2_gfblup_prediction_all.rds")
+saveRDS(T16_2_gfblup_variances_all,"T16_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_3_gblup_prediction_all_1_1000=readRDS(file="T16_3_gblup_prediction_all_1_1000.rds")
+T16_3_gblup_prediction_all_1001_2000=readRDS(file="T16_3_gblup_prediction_all_1001_2000.rds")
+T16_3_gblup_prediction_all_2001_3000=readRDS(file="T16_3_gblup_prediction_all_2001_3000.rds")
+T16_3_gblup_prediction_all_3001_4000=readRDS(file="T16_3_gblup_prediction_all_3001_4000.rds")
+T16_3_gblup_prediction_all_4001_5000=readRDS(file="T16_3_gblup_prediction_all_4001_5000.rds")
+T16_3_gblup_prediction_all_5001_6000=readRDS(file="T16_3_gblup_prediction_all_5001_6000.rds")
+T16_3_gblup_prediction_all_6001_7297=readRDS(file="T16_3_gblup_prediction_all_6001_7297.rds")
+T16_3_gblup_prediction_all=c(T16_3_gblup_prediction_all_1_1000,T16_3_gblup_prediction_all_1001_2000,T16_3_gblup_prediction_all_2001_3000,T16_3_gblup_prediction_all_3001_4000,T16_3_gblup_prediction_all_4001_5000,T16_3_gblup_prediction_all_5001_6000,T16_3_gblup_prediction_all_6001_7297)
+
+T16_3_gblup_variances_all_1_1000=readRDS(file="T16_3_gblup_variances_all_1_1000.rds")
+T16_3_gblup_variances_all_1001_2000=readRDS(file="T16_3_gblup_variances_all_1001_2000.rds")
+T16_3_gblup_variances_all_2001_3000=readRDS(file="T16_3_gblup_variances_all_2001_3000.rds")
+T16_3_gblup_variances_all_3001_4000=readRDS(file="T16_3_gblup_variances_all_3001_4000.rds")
+T16_3_gblup_variances_all_4001_5000=readRDS(file="T16_3_gblup_variances_all_4001_5000.rds")
+T16_3_gblup_variances_all_5001_6000=readRDS(file="T16_3_gblup_variances_all_5001_6000.rds")
+T16_3_gblup_variances_all_6001_7297=readRDS(file="T16_3_gblup_variances_all_6001_7297.rds")
+T16_3_gblup_variances_all=c(T16_3_gblup_variances_all_1_1000,T16_3_gblup_variances_all_1001_2000,T16_3_gblup_variances_all_2001_3000,T16_3_gblup_variances_all_3001_4000,T16_3_gblup_variances_all_4001_5000,T16_3_gblup_variances_all_5001_6000,T16_3_gblup_variances_all_6001_7297)
+
+saveRDS(T16_3_gblup_prediction_all,"T16_3_gblup_prediction_all.rds")
+saveRDS(T16_3_gblup_variances_all,"T16_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_3_gfblup_prediction_all_1_1000=readRDS(file="T16_3_gfblup_prediction_all_1_1000.rds")
+T16_3_gfblup_prediction_all_1001_2000=readRDS(file="T16_3_gfblup_prediction_all_1001_2000.rds")
+T16_3_gfblup_prediction_all_2001_3000=readRDS(file="T16_3_gfblup_prediction_all_2001_3000.rds")
+T16_3_gfblup_prediction_all_3001_4000=readRDS(file="T16_3_gfblup_prediction_all_3001_4000.rds")
+T16_3_gfblup_prediction_all_4001_5000=readRDS(file="T16_3_gfblup_prediction_all_4001_5000.rds")
+T16_3_gfblup_prediction_all_5001_6000=readRDS(file="T16_3_gfblup_prediction_all_5001_6000.rds")
+T16_3_gfblup_prediction_all_6001_7297=readRDS(file="T16_3_gfblup_prediction_all_6001_7297.rds")
+
+T16_3_gfblup_variances_all_1_1000=readRDS(file="T16_3_gfblup_variances_all_1_1000.rds")
+T16_3_gfblup_variances_all_1001_2000=readRDS(file="T16_3_gfblup_variances_all_1001_2000.rds")
+T16_3_gfblup_variances_all_2001_3000=readRDS(file="T16_3_gfblup_variances_all_2001_3000.rds")
+T16_3_gfblup_variances_all_3001_4000=readRDS(file="T16_3_gfblup_variances_all_3001_4000.rds")
+T16_3_gfblup_variances_all_4001_5000=readRDS(file="T16_3_gfblup_variances_all_4001_5000.rds")
+T16_3_gfblup_variances_all_5001_6000=readRDS(file="T16_3_gfblup_variances_all_5001_6000.rds")
+T16_3_gfblup_variances_all_6001_7297=readRDS(file="T16_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T16_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_3_gfblup_variances_all=rep(list(list()),cycles)
+T16_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_1_1000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_1001_2000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_2001_3000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_3001_4000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_4001_5000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_5001_6000[[r]])
+	T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_6001_7297[[r]])
+
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_1_1000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_1001_2000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_2001_3000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_3001_4000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_4001_5000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_5001_6000[[r]])
+	T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T16_3_gfblup_prediction_all,"T16_3_gfblup_prediction_all.rds")
+saveRDS(T16_3_gfblup_variances_all,"T16_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_4_gblup_prediction_all_1_1000=readRDS(file="T16_4_gblup_prediction_all_1_1000.rds")
+T16_4_gblup_prediction_all_1001_2000=readRDS(file="T16_4_gblup_prediction_all_1001_2000.rds")
+T16_4_gblup_prediction_all_2001_3000=readRDS(file="T16_4_gblup_prediction_all_2001_3000.rds")
+T16_4_gblup_prediction_all_3001_4000=readRDS(file="T16_4_gblup_prediction_all_3001_4000.rds")
+T16_4_gblup_prediction_all_4001_5000=readRDS(file="T16_4_gblup_prediction_all_4001_5000.rds")
+T16_4_gblup_prediction_all_5001_6000=readRDS(file="T16_4_gblup_prediction_all_5001_6000.rds")
+T16_4_gblup_prediction_all_6001_7297=readRDS(file="T16_4_gblup_prediction_all_6001_7297.rds")
+T16_4_gblup_prediction_all=c(T16_4_gblup_prediction_all_1_1000,T16_4_gblup_prediction_all_1001_2000,T16_4_gblup_prediction_all_2001_3000,T16_4_gblup_prediction_all_3001_4000,T16_4_gblup_prediction_all_4001_5000,T16_4_gblup_prediction_all_5001_6000,T16_4_gblup_prediction_all_6001_7297)
+
+T16_4_gblup_variances_all_1_1000=readRDS(file="T16_4_gblup_variances_all_1_1000.rds")
+T16_4_gblup_variances_all_1001_2000=readRDS(file="T16_4_gblup_variances_all_1001_2000.rds")
+T16_4_gblup_variances_all_2001_3000=readRDS(file="T16_4_gblup_variances_all_2001_3000.rds")
+T16_4_gblup_variances_all_3001_4000=readRDS(file="T16_4_gblup_variances_all_3001_4000.rds")
+T16_4_gblup_variances_all_4001_5000=readRDS(file="T16_4_gblup_variances_all_4001_5000.rds")
+T16_4_gblup_variances_all_5001_6000=readRDS(file="T16_4_gblup_variances_all_5001_6000.rds")
+T16_4_gblup_variances_all_6001_7297=readRDS(file="T16_4_gblup_variances_all_6001_7297.rds")
+T16_4_gblup_variances_all=c(T16_4_gblup_variances_all_1_1000,T16_4_gblup_variances_all_1001_2000,T16_4_gblup_variances_all_2001_3000,T16_4_gblup_variances_all_3001_4000,T16_4_gblup_variances_all_4001_5000,T16_4_gblup_variances_all_5001_6000,T16_4_gblup_variances_all_6001_7297)
+
+saveRDS(T16_4_gblup_prediction_all,"T16_4_gblup_prediction_all.rds")
+saveRDS(T16_4_gblup_variances_all,"T16_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_4_gfblup_prediction_all_1_1000=readRDS(file="T16_4_gfblup_prediction_all_1_1000.rds")
+T16_4_gfblup_prediction_all_1001_2000=readRDS(file="T16_4_gfblup_prediction_all_1001_2000.rds")
+T16_4_gfblup_prediction_all_2001_3000=readRDS(file="T16_4_gfblup_prediction_all_2001_3000.rds")
+T16_4_gfblup_prediction_all_3001_4000=readRDS(file="T16_4_gfblup_prediction_all_3001_4000.rds")
+T16_4_gfblup_prediction_all_4001_5000=readRDS(file="T16_4_gfblup_prediction_all_4001_5000.rds")
+T16_4_gfblup_prediction_all_5001_6000=readRDS(file="T16_4_gfblup_prediction_all_5001_6000.rds")
+T16_4_gfblup_prediction_all_6001_7297=readRDS(file="T16_4_gfblup_prediction_all_6001_7297.rds")
+
+T16_4_gfblup_variances_all_1_1000=readRDS(file="T16_4_gfblup_variances_all_1_1000.rds")
+T16_4_gfblup_variances_all_1001_2000=readRDS(file="T16_4_gfblup_variances_all_1001_2000.rds")
+T16_4_gfblup_variances_all_2001_3000=readRDS(file="T16_4_gfblup_variances_all_2001_3000.rds")
+T16_4_gfblup_variances_all_3001_4000=readRDS(file="T16_4_gfblup_variances_all_3001_4000.rds")
+T16_4_gfblup_variances_all_4001_5000=readRDS(file="T16_4_gfblup_variances_all_4001_5000.rds")
+T16_4_gfblup_variances_all_5001_6000=readRDS(file="T16_4_gfblup_variances_all_5001_6000.rds")
+T16_4_gfblup_variances_all_6001_7297=readRDS(file="T16_4_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T16_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_4_gfblup_variances_all=rep(list(list()),cycles)
+T16_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_1_1000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_1001_2000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_2001_3000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_3001_4000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_4001_5000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_5001_6000[[r]])
+	T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_6001_7297[[r]])
+
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_1_1000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_1001_2000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_2001_3000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_3001_4000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_4001_5000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_5001_6000[[r]])
+	T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T16_4_gfblup_prediction_all,"T16_4_gfblup_prediction_all.rds")
+saveRDS(T16_4_gfblup_variances_all,"T16_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_5_gblup_prediction_all_1_1000=readRDS(file="T16_5_gblup_prediction_all_1_1000.rds")
+T16_5_gblup_prediction_all_1001_2000=readRDS(file="T16_5_gblup_prediction_all_1001_2000.rds")
+T16_5_gblup_prediction_all_2001_3000=readRDS(file="T16_5_gblup_prediction_all_2001_3000.rds")
+T16_5_gblup_prediction_all_3001_4000=readRDS(file="T16_5_gblup_prediction_all_3001_4000.rds")
+T16_5_gblup_prediction_all_4001_5000=readRDS(file="T16_5_gblup_prediction_all_4001_5000.rds")
+T16_5_gblup_prediction_all_5001_6000=readRDS(file="T16_5_gblup_prediction_all_5001_6000.rds")
+T16_5_gblup_prediction_all_6001_7297=readRDS(file="T16_5_gblup_prediction_all_6001_7297.rds")
+T16_5_gblup_prediction_all=c(T16_5_gblup_prediction_all_1_1000,T16_5_gblup_prediction_all_1001_2000,T16_5_gblup_prediction_all_2001_3000,T16_5_gblup_prediction_all_3001_4000,T16_5_gblup_prediction_all_4001_5000,T16_5_gblup_prediction_all_5001_6000,T16_5_gblup_prediction_all_6001_7297)
+
+T16_5_gblup_variances_all_1_1000=readRDS(file="T16_5_gblup_variances_all_1_1000.rds")
+T16_5_gblup_variances_all_1001_2000=readRDS(file="T16_5_gblup_variances_all_1001_2000.rds")
+T16_5_gblup_variances_all_2001_3000=readRDS(file="T16_5_gblup_variances_all_2001_3000.rds")
+T16_5_gblup_variances_all_3001_4000=readRDS(file="T16_5_gblup_variances_all_3001_4000.rds")
+T16_5_gblup_variances_all_4001_5000=readRDS(file="T16_5_gblup_variances_all_4001_5000.rds")
+T16_5_gblup_variances_all_5001_6000=readRDS(file="T16_5_gblup_variances_all_5001_6000.rds")
+T16_5_gblup_variances_all_6001_7297=readRDS(file="T16_5_gblup_variances_all_6001_7297.rds")
+T16_5_gblup_variances_all=c(T16_5_gblup_variances_all_1_1000,T16_5_gblup_variances_all_1001_2000,T16_5_gblup_variances_all_2001_3000,T16_5_gblup_variances_all_3001_4000,T16_5_gblup_variances_all_4001_5000,T16_5_gblup_variances_all_5001_6000,T16_5_gblup_variances_all_6001_7297)
+
+saveRDS(T16_5_gblup_prediction_all,"T16_5_gblup_prediction_all.rds")
+saveRDS(T16_5_gblup_variances_all,"T16_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_5_gfblup_prediction_all_1_1000=readRDS(file="T16_5_gfblup_prediction_all_1_1000.rds")
+T16_5_gfblup_prediction_all_1001_2000=readRDS(file="T16_5_gfblup_prediction_all_1001_2000.rds")
+T16_5_gfblup_prediction_all_2001_3000=readRDS(file="T16_5_gfblup_prediction_all_2001_3000.rds")
+T16_5_gfblup_prediction_all_3001_4000=readRDS(file="T16_5_gfblup_prediction_all_3001_4000.rds")
+T16_5_gfblup_prediction_all_4001_5000=readRDS(file="T16_5_gfblup_prediction_all_4001_5000.rds")
+T16_5_gfblup_prediction_all_5001_6000=readRDS(file="T16_5_gfblup_prediction_all_5001_6000.rds")
+T16_5_gfblup_prediction_all_6001_7297=readRDS(file="T16_5_gfblup_prediction_all_6001_7297.rds")
+
+T16_5_gfblup_variances_all_1_1000=readRDS(file="T16_5_gfblup_variances_all_1_1000.rds")
+T16_5_gfblup_variances_all_1001_2000=readRDS(file="T16_5_gfblup_variances_all_1001_2000.rds")
+T16_5_gfblup_variances_all_2001_3000=readRDS(file="T16_5_gfblup_variances_all_2001_3000.rds")
+T16_5_gfblup_variances_all_3001_4000=readRDS(file="T16_5_gfblup_variances_all_3001_4000.rds")
+T16_5_gfblup_variances_all_4001_5000=readRDS(file="T16_5_gfblup_variances_all_4001_5000.rds")
+T16_5_gfblup_variances_all_5001_6000=readRDS(file="T16_5_gfblup_variances_all_5001_6000.rds")
+T16_5_gfblup_variances_all_6001_7297=readRDS(file="T16_5_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T16_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_5_gfblup_variances_all=rep(list(list()),cycles)
+T16_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_1_1000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_1001_2000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_2001_3000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_3001_4000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_4001_5000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_5001_6000[[r]])
+	T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_6001_7297[[r]])
+
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_1_1000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_1001_2000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_2001_3000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_3001_4000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_4001_5000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_5001_6000[[r]])
+	T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T16_5_gfblup_prediction_all,"T16_5_gfblup_prediction_all.rds")
+saveRDS(T16_5_gfblup_variances_all,"T16_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_6_gblup_prediction_all_1_1000=readRDS(file="T16_6_gblup_prediction_all_1_1000.rds")
+T16_6_gblup_prediction_all_1001_2000=readRDS(file="T16_6_gblup_prediction_all_1001_2000.rds")
+T16_6_gblup_prediction_all_2001_3000=readRDS(file="T16_6_gblup_prediction_all_2001_3000.rds")
+T16_6_gblup_prediction_all_3001_4000=readRDS(file="T16_6_gblup_prediction_all_3001_4000.rds")
+T16_6_gblup_prediction_all_4001_5000=readRDS(file="T16_6_gblup_prediction_all_4001_5000.rds")
+T16_6_gblup_prediction_all_5001_6000=readRDS(file="T16_6_gblup_prediction_all_5001_6000.rds")
+T16_6_gblup_prediction_all_6001_7297=readRDS(file="T16_6_gblup_prediction_all_6001_7297.rds")
+T16_6_gblup_prediction_all=c(T16_6_gblup_prediction_all_1_1000,T16_6_gblup_prediction_all_1001_2000,T16_6_gblup_prediction_all_2001_3000,T16_6_gblup_prediction_all_3001_4000,T16_6_gblup_prediction_all_4001_5000,T16_6_gblup_prediction_all_5001_6000,T16_6_gblup_prediction_all_6001_7297)
+
+T16_6_gblup_variances_all_1_1000=readRDS(file="T16_6_gblup_variances_all_1_1000.rds")
+T16_6_gblup_variances_all_1001_2000=readRDS(file="T16_6_gblup_variances_all_1001_2000.rds")
+T16_6_gblup_variances_all_2001_3000=readRDS(file="T16_6_gblup_variances_all_2001_3000.rds")
+T16_6_gblup_variances_all_3001_4000=readRDS(file="T16_6_gblup_variances_all_3001_4000.rds")
+T16_6_gblup_variances_all_4001_5000=readRDS(file="T16_6_gblup_variances_all_4001_5000.rds")
+T16_6_gblup_variances_all_5001_6000=readRDS(file="T16_6_gblup_variances_all_5001_6000.rds")
+T16_6_gblup_variances_all_6001_7297=readRDS(file="T16_6_gblup_variances_all_6001_7297.rds")
+T16_6_gblup_variances_all=c(T16_6_gblup_variances_all_1_1000,T16_6_gblup_variances_all_1001_2000,T16_6_gblup_variances_all_2001_3000,T16_6_gblup_variances_all_3001_4000,T16_6_gblup_variances_all_4001_5000,T16_6_gblup_variances_all_5001_6000,T16_6_gblup_variances_all_6001_7297)
+
+saveRDS(T16_6_gblup_prediction_all,"T16_6_gblup_prediction_all.rds")
+saveRDS(T16_6_gblup_variances_all,"T16_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_6_gfblup_prediction_all_1_1000=readRDS(file="T16_6_gfblup_prediction_all_1_1000.rds")
+T16_6_gfblup_prediction_all_1001_2000=readRDS(file="T16_6_gfblup_prediction_all_1001_2000.rds")
+T16_6_gfblup_prediction_all_2001_3000=readRDS(file="T16_6_gfblup_prediction_all_2001_3000.rds")
+T16_6_gfblup_prediction_all_3001_4000=readRDS(file="T16_6_gfblup_prediction_all_3001_4000.rds")
+T16_6_gfblup_prediction_all_4001_5000=readRDS(file="T16_6_gfblup_prediction_all_4001_5000.rds")
+T16_6_gfblup_prediction_all_5001_6000=readRDS(file="T16_6_gfblup_prediction_all_5001_6000.rds")
+T16_6_gfblup_prediction_all_6001_7297=readRDS(file="T16_6_gfblup_prediction_all_6001_7297.rds")
+
+T16_6_gfblup_variances_all_1_1000=readRDS(file="T16_6_gfblup_variances_all_1_1000.rds")
+T16_6_gfblup_variances_all_1001_2000=readRDS(file="T16_6_gfblup_variances_all_1001_2000.rds")
+T16_6_gfblup_variances_all_2001_3000=readRDS(file="T16_6_gfblup_variances_all_2001_3000.rds")
+T16_6_gfblup_variances_all_3001_4000=readRDS(file="T16_6_gfblup_variances_all_3001_4000.rds")
+T16_6_gfblup_variances_all_4001_5000=readRDS(file="T16_6_gfblup_variances_all_4001_5000.rds")
+T16_6_gfblup_variances_all_5001_6000=readRDS(file="T16_6_gfblup_variances_all_5001_6000.rds")
+T16_6_gfblup_variances_all_6001_7297=readRDS(file="T16_6_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T16_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_6_gfblup_variances_all=rep(list(list()),cycles)
+T16_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_1_1000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_1001_2000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_2001_3000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_3001_4000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_4001_5000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_5001_6000[[r]])
+	T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_6001_7297[[r]])
+
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_1_1000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_1001_2000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_2001_3000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_3001_4000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_4001_5000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_5001_6000[[r]])
+	T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T16_6_gfblup_prediction_all,"T16_6_gfblup_prediction_all.rds")
+saveRDS(T16_6_gfblup_variances_all,"T16_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_7_gblup_prediction_all_1_1000=readRDS(file="T16_7_gblup_prediction_all_1_1000.rds")
+T16_7_gblup_prediction_all_1001_2000=readRDS(file="T16_7_gblup_prediction_all_1001_2000.rds")
+T16_7_gblup_prediction_all_2001_3000=readRDS(file="T16_7_gblup_prediction_all_2001_3000.rds")
+T16_7_gblup_prediction_all_3001_4000=readRDS(file="T16_7_gblup_prediction_all_3001_4000.rds")
+T16_7_gblup_prediction_all_4001_5000=readRDS(file="T16_7_gblup_prediction_all_4001_5000.rds")
+T16_7_gblup_prediction_all_5001_6000=readRDS(file="T16_7_gblup_prediction_all_5001_6000.rds")
+T16_7_gblup_prediction_all_6001_7297=readRDS(file="T16_7_gblup_prediction_all_6001_7297.rds")
+T16_7_gblup_prediction_all=c(T16_7_gblup_prediction_all_1_1000,T16_7_gblup_prediction_all_1001_2000,T16_7_gblup_prediction_all_2001_3000,T16_7_gblup_prediction_all_3001_4000,T16_7_gblup_prediction_all_4001_5000,T16_7_gblup_prediction_all_5001_6000,T16_7_gblup_prediction_all_6001_7297)
+
+T16_7_gblup_variances_all_1_1000=readRDS(file="T16_7_gblup_variances_all_1_1000.rds")
+T16_7_gblup_variances_all_1001_2000=readRDS(file="T16_7_gblup_variances_all_1001_2000.rds")
+T16_7_gblup_variances_all_2001_3000=readRDS(file="T16_7_gblup_variances_all_2001_3000.rds")
+T16_7_gblup_variances_all_3001_4000=readRDS(file="T16_7_gblup_variances_all_3001_4000.rds")
+T16_7_gblup_variances_all_4001_5000=readRDS(file="T16_7_gblup_variances_all_4001_5000.rds")
+T16_7_gblup_variances_all_5001_6000=readRDS(file="T16_7_gblup_variances_all_5001_6000.rds")
+T16_7_gblup_variances_all_6001_7297=readRDS(file="T16_7_gblup_variances_all_6001_7297.rds")
+T16_7_gblup_variances_all=c(T16_7_gblup_variances_all_1_1000,T16_7_gblup_variances_all_1001_2000,T16_7_gblup_variances_all_2001_3000,T16_7_gblup_variances_all_3001_4000,T16_7_gblup_variances_all_4001_5000,T16_7_gblup_variances_all_5001_6000,T16_7_gblup_variances_all_6001_7297)
+
+saveRDS(T16_7_gblup_prediction_all,"T16_7_gblup_prediction_all.rds")
+saveRDS(T16_7_gblup_variances_all,"T16_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_7_gfblup_prediction_all_1_1000=readRDS(file="T16_7_gfblup_prediction_all_1_1000.rds")
+T16_7_gfblup_prediction_all_1001_2000=readRDS(file="T16_7_gfblup_prediction_all_1001_2000.rds")
+T16_7_gfblup_prediction_all_2001_3000=readRDS(file="T16_7_gfblup_prediction_all_2001_3000.rds")
+T16_7_gfblup_prediction_all_3001_4000=readRDS(file="T16_7_gfblup_prediction_all_3001_4000.rds")
+T16_7_gfblup_prediction_all_4001_5000=readRDS(file="T16_7_gfblup_prediction_all_4001_5000.rds")
+T16_7_gfblup_prediction_all_5001_6000=readRDS(file="T16_7_gfblup_prediction_all_5001_6000.rds")
+T16_7_gfblup_prediction_all_6001_7297=readRDS(file="T16_7_gfblup_prediction_all_6001_7297.rds")
+
+T16_7_gfblup_variances_all_1_1000=readRDS(file="T16_7_gfblup_variances_all_1_1000.rds")
+T16_7_gfblup_variances_all_1001_2000=readRDS(file="T16_7_gfblup_variances_all_1001_2000.rds")
+T16_7_gfblup_variances_all_2001_3000=readRDS(file="T16_7_gfblup_variances_all_2001_3000.rds")
+T16_7_gfblup_variances_all_3001_4000=readRDS(file="T16_7_gfblup_variances_all_3001_4000.rds")
+T16_7_gfblup_variances_all_4001_5000=readRDS(file="T16_7_gfblup_variances_all_4001_5000.rds")
+T16_7_gfblup_variances_all_5001_6000=readRDS(file="T16_7_gfblup_variances_all_5001_6000.rds")
+T16_7_gfblup_variances_all_6001_7297=readRDS(file="T16_7_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T16_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_7_gfblup_variances_all=rep(list(list()),cycles)
+T16_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_1_1000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_1001_2000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_2001_3000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_3001_4000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_4001_5000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_5001_6000[[r]])
+	T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_6001_7297[[r]])
+
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_1_1000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_1001_2000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_2001_3000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_3001_4000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_4001_5000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_5001_6000[[r]])
+	T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T16_7_gfblup_prediction_all,"T16_7_gfblup_prediction_all.rds")
+saveRDS(T16_7_gfblup_variances_all,"T16_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_8_gblup_prediction_all_1_1000=readRDS(file="T16_8_gblup_prediction_all_1_1000.rds")
+T16_8_gblup_prediction_all_1001_2000=readRDS(file="T16_8_gblup_prediction_all_1001_2000.rds")
+T16_8_gblup_prediction_all_2001_3000=readRDS(file="T16_8_gblup_prediction_all_2001_3000.rds")
+T16_8_gblup_prediction_all_3001_4000=readRDS(file="T16_8_gblup_prediction_all_3001_4000.rds")
+T16_8_gblup_prediction_all_4001_5000=readRDS(file="T16_8_gblup_prediction_all_4001_5000.rds")
+T16_8_gblup_prediction_all_5001_6000=readRDS(file="T16_8_gblup_prediction_all_5001_6000.rds")
+T16_8_gblup_prediction_all_6001_7297=readRDS(file="T16_8_gblup_prediction_all_6001_7297.rds")
+T16_8_gblup_prediction_all=c(T16_8_gblup_prediction_all_1_1000,T16_8_gblup_prediction_all_1001_2000,T16_8_gblup_prediction_all_2001_3000,T16_8_gblup_prediction_all_3001_4000,T16_8_gblup_prediction_all_4001_5000,T16_8_gblup_prediction_all_5001_6000,T16_8_gblup_prediction_all_6001_7297)
+
+T16_8_gblup_variances_all_1_1000=readRDS(file="T16_8_gblup_variances_all_1_1000.rds")
+T16_8_gblup_variances_all_1001_2000=readRDS(file="T16_8_gblup_variances_all_1001_2000.rds")
+T16_8_gblup_variances_all_2001_3000=readRDS(file="T16_8_gblup_variances_all_2001_3000.rds")
+T16_8_gblup_variances_all_3001_4000=readRDS(file="T16_8_gblup_variances_all_3001_4000.rds")
+T16_8_gblup_variances_all_4001_5000=readRDS(file="T16_8_gblup_variances_all_4001_5000.rds")
+T16_8_gblup_variances_all_5001_6000=readRDS(file="T16_8_gblup_variances_all_5001_6000.rds")
+T16_8_gblup_variances_all_6001_7297=readRDS(file="T16_8_gblup_variances_all_6001_7297.rds")
+T16_8_gblup_variances_all=c(T16_8_gblup_variances_all_1_1000,T16_8_gblup_variances_all_1001_2000,T16_8_gblup_variances_all_2001_3000,T16_8_gblup_variances_all_3001_4000,T16_8_gblup_variances_all_4001_5000,T16_8_gblup_variances_all_5001_6000,T16_8_gblup_variances_all_6001_7297)
+
+saveRDS(T16_8_gblup_prediction_all,"T16_8_gblup_prediction_all.rds")
+saveRDS(T16_8_gblup_variances_all,"T16_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T16_8_gfblup_prediction_all_1_1000=readRDS(file="T16_8_gfblup_prediction_all_1_1000.rds")
+T16_8_gfblup_prediction_all_1001_2000=readRDS(file="T16_8_gfblup_prediction_all_1001_2000.rds")
+T16_8_gfblup_prediction_all_2001_3000=readRDS(file="T16_8_gfblup_prediction_all_2001_3000.rds")
+T16_8_gfblup_prediction_all_3001_4000=readRDS(file="T16_8_gfblup_prediction_all_3001_4000.rds")
+T16_8_gfblup_prediction_all_4001_5000=readRDS(file="T16_8_gfblup_prediction_all_4001_5000.rds")
+T16_8_gfblup_prediction_all_5001_6000=readRDS(file="T16_8_gfblup_prediction_all_5001_6000.rds")
+T16_8_gfblup_prediction_all_6001_7297=readRDS(file="T16_8_gfblup_prediction_all_6001_7297.rds")
+
+T16_8_gfblup_variances_all_1_1000=readRDS(file="T16_8_gfblup_variances_all_1_1000.rds")
+T16_8_gfblup_variances_all_1001_2000=readRDS(file="T16_8_gfblup_variances_all_1001_2000.rds")
+T16_8_gfblup_variances_all_2001_3000=readRDS(file="T16_8_gfblup_variances_all_2001_3000.rds")
+T16_8_gfblup_variances_all_3001_4000=readRDS(file="T16_8_gfblup_variances_all_3001_4000.rds")
+T16_8_gfblup_variances_all_4001_5000=readRDS(file="T16_8_gfblup_variances_all_4001_5000.rds")
+T16_8_gfblup_variances_all_5001_6000=readRDS(file="T16_8_gfblup_variances_all_5001_6000.rds")
+T16_8_gfblup_variances_all_6001_7297=readRDS(file="T16_8_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T16_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T16_8_gfblup_variances_all=rep(list(list()),cycles)
+T16_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_1_1000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_1001_2000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_2001_3000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_3001_4000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_4001_5000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_5001_6000[[r]])
+	T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_6001_7297[[r]])
+
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_1_1000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_1001_2000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_2001_3000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_3001_4000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_4001_5000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_5001_6000[[r]])
+	T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T16_8_gfblup_prediction_all,"T16_8_gfblup_prediction_all.rds")
+saveRDS(T16_8_gfblup_variances_all,"T16_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_1_gblup_prediction_all_1_1000=readRDS(file="T17_1_gblup_prediction_all_1_1000.rds")
+T17_1_gblup_prediction_all_1001_2000=readRDS(file="T17_1_gblup_prediction_all_1001_2000.rds")
+T17_1_gblup_prediction_all_2001_3000=readRDS(file="T17_1_gblup_prediction_all_2001_3000.rds")
+T17_1_gblup_prediction_all_3001_4000=readRDS(file="T17_1_gblup_prediction_all_3001_4000.rds")
+T17_1_gblup_prediction_all_4001_5000=readRDS(file="T17_1_gblup_prediction_all_4001_5000.rds")
+T17_1_gblup_prediction_all_5001_6000=readRDS(file="T17_1_gblup_prediction_all_5001_6000.rds")
+T17_1_gblup_prediction_all_6001_7297=readRDS(file="T17_1_gblup_prediction_all_6001_7297.rds")
+T17_1_gblup_prediction_all=c(T17_1_gblup_prediction_all_1_1000,T17_1_gblup_prediction_all_1001_2000,T17_1_gblup_prediction_all_2001_3000,T17_1_gblup_prediction_all_3001_4000,T17_1_gblup_prediction_all_4001_5000,T17_1_gblup_prediction_all_5001_6000,T17_1_gblup_prediction_all_6001_7297)
+
+T17_1_gblup_variances_all_1_1000=readRDS(file="T17_1_gblup_variances_all_1_1000.rds")
+T17_1_gblup_variances_all_1001_2000=readRDS(file="T17_1_gblup_variances_all_1001_2000.rds")
+T17_1_gblup_variances_all_2001_3000=readRDS(file="T17_1_gblup_variances_all_2001_3000.rds")
+T17_1_gblup_variances_all_3001_4000=readRDS(file="T17_1_gblup_variances_all_3001_4000.rds")
+T17_1_gblup_variances_all_4001_5000=readRDS(file="T17_1_gblup_variances_all_4001_5000.rds")
+T17_1_gblup_variances_all_5001_6000=readRDS(file="T17_1_gblup_variances_all_5001_6000.rds")
+T17_1_gblup_variances_all_6001_7297=readRDS(file="T17_1_gblup_variances_all_6001_7297.rds")
+T17_1_gblup_variances_all=c(T17_1_gblup_variances_all_1_1000,T17_1_gblup_variances_all_1001_2000,T17_1_gblup_variances_all_2001_3000,T17_1_gblup_variances_all_3001_4000,T17_1_gblup_variances_all_4001_5000,T17_1_gblup_variances_all_5001_6000,T17_1_gblup_variances_all_6001_7297)
+
+saveRDS(T17_1_gblup_prediction_all,"T17_1_gblup_prediction_all.rds")
+saveRDS(T17_1_gblup_variances_all,"T17_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_1_gfblup_prediction_all_1_1000=readRDS(file="T17_1_gfblup_prediction_all_1_1000.rds")
+T17_1_gfblup_prediction_all_1001_2000=readRDS(file="T17_1_gfblup_prediction_all_1001_2000.rds")
+T17_1_gfblup_prediction_all_2001_3000=readRDS(file="T17_1_gfblup_prediction_all_2001_3000.rds")
+T17_1_gfblup_prediction_all_3001_4000=readRDS(file="T17_1_gfblup_prediction_all_3001_4000.rds")
+T17_1_gfblup_prediction_all_4001_5000=readRDS(file="T17_1_gfblup_prediction_all_4001_5000.rds")
+T17_1_gfblup_prediction_all_5001_6000=readRDS(file="T17_1_gfblup_prediction_all_5001_6000.rds")
+T17_1_gfblup_prediction_all_6001_7297=readRDS(file="T17_1_gfblup_prediction_all_6001_7297.rds")
+
+T17_1_gfblup_variances_all_1_1000=readRDS(file="T17_1_gfblup_variances_all_1_1000.rds")
+T17_1_gfblup_variances_all_1001_2000=readRDS(file="T17_1_gfblup_variances_all_1001_2000.rds")
+T17_1_gfblup_variances_all_2001_3000=readRDS(file="T17_1_gfblup_variances_all_2001_3000.rds")
+T17_1_gfblup_variances_all_3001_4000=readRDS(file="T17_1_gfblup_variances_all_3001_4000.rds")
+T17_1_gfblup_variances_all_4001_5000=readRDS(file="T17_1_gfblup_variances_all_4001_5000.rds")
+T17_1_gfblup_variances_all_5001_6000=readRDS(file="T17_1_gfblup_variances_all_5001_6000.rds")
+T17_1_gfblup_variances_all_6001_7297=readRDS(file="T17_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T17_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_1_gfblup_variances_all=rep(list(list()),cycles)
+T17_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_1_1000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_1001_2000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_2001_3000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_3001_4000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_4001_5000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_5001_6000[[r]])
+	T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_6001_7297[[r]])
+
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_1_1000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_1001_2000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_2001_3000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_3001_4000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_4001_5000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_5001_6000[[r]])
+	T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T17_1_gfblup_prediction_all,"T17_1_gfblup_prediction_all.rds")
+saveRDS(T17_1_gfblup_variances_all,"T17_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_2_gblup_prediction_all_1_1000=readRDS(file="T17_2_gblup_prediction_all_1_1000.rds")
+T17_2_gblup_prediction_all_1001_2000=readRDS(file="T17_2_gblup_prediction_all_1001_2000.rds")
+T17_2_gblup_prediction_all_2001_3000=readRDS(file="T17_2_gblup_prediction_all_2001_3000.rds")
+T17_2_gblup_prediction_all_3001_4000=readRDS(file="T17_2_gblup_prediction_all_3001_4000.rds")
+T17_2_gblup_prediction_all_4001_5000=readRDS(file="T17_2_gblup_prediction_all_4001_5000.rds")
+T17_2_gblup_prediction_all_5001_6000=readRDS(file="T17_2_gblup_prediction_all_5001_6000.rds")
+T17_2_gblup_prediction_all_6001_7297=readRDS(file="T17_2_gblup_prediction_all_6001_7297.rds")
+T17_2_gblup_prediction_all=c(T17_2_gblup_prediction_all_1_1000,T17_2_gblup_prediction_all_1001_2000,T17_2_gblup_prediction_all_2001_3000,T17_2_gblup_prediction_all_3001_4000,T17_2_gblup_prediction_all_4001_5000,T17_2_gblup_prediction_all_5001_6000,T17_2_gblup_prediction_all_6001_7297)
+
+T17_2_gblup_variances_all_1_1000=readRDS(file="T17_2_gblup_variances_all_1_1000.rds")
+T17_2_gblup_variances_all_1001_2000=readRDS(file="T17_2_gblup_variances_all_1001_2000.rds")
+T17_2_gblup_variances_all_2001_3000=readRDS(file="T17_2_gblup_variances_all_2001_3000.rds")
+T17_2_gblup_variances_all_3001_4000=readRDS(file="T17_2_gblup_variances_all_3001_4000.rds")
+T17_2_gblup_variances_all_4001_5000=readRDS(file="T17_2_gblup_variances_all_4001_5000.rds")
+T17_2_gblup_variances_all_5001_6000=readRDS(file="T17_2_gblup_variances_all_5001_6000.rds")
+T17_2_gblup_variances_all_6001_7297=readRDS(file="T17_2_gblup_variances_all_6001_7297.rds")
+T17_2_gblup_variances_all=c(T17_2_gblup_variances_all_1_1000,T17_2_gblup_variances_all_1001_2000,T17_2_gblup_variances_all_2001_3000,T17_2_gblup_variances_all_3001_4000,T17_2_gblup_variances_all_4001_5000,T17_2_gblup_variances_all_5001_6000,T17_2_gblup_variances_all_6001_7297)
+
+saveRDS(T17_2_gblup_prediction_all,"T17_2_gblup_prediction_all.rds")
+saveRDS(T17_2_gblup_variances_all,"T17_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_2_gfblup_prediction_all_1_1000=readRDS(file="T17_2_gfblup_prediction_all_1_1000.rds")
+T17_2_gfblup_prediction_all_1001_2000=readRDS(file="T17_2_gfblup_prediction_all_1001_2000.rds")
+T17_2_gfblup_prediction_all_2001_3000=readRDS(file="T17_2_gfblup_prediction_all_2001_3000.rds")
+T17_2_gfblup_prediction_all_3001_4000=readRDS(file="T17_2_gfblup_prediction_all_3001_4000.rds")
+T17_2_gfblup_prediction_all_4001_5000=readRDS(file="T17_2_gfblup_prediction_all_4001_5000.rds")
+T17_2_gfblup_prediction_all_5001_6000=readRDS(file="T17_2_gfblup_prediction_all_5001_6000.rds")
+T17_2_gfblup_prediction_all_6001_7297=readRDS(file="T17_2_gfblup_prediction_all_6001_7297.rds")
+
+T17_2_gfblup_variances_all_1_1000=readRDS(file="T17_2_gfblup_variances_all_1_1000.rds")
+T17_2_gfblup_variances_all_1001_2000=readRDS(file="T17_2_gfblup_variances_all_1001_2000.rds")
+T17_2_gfblup_variances_all_2001_3000=readRDS(file="T17_2_gfblup_variances_all_2001_3000.rds")
+T17_2_gfblup_variances_all_3001_4000=readRDS(file="T17_2_gfblup_variances_all_3001_4000.rds")
+T17_2_gfblup_variances_all_4001_5000=readRDS(file="T17_2_gfblup_variances_all_4001_5000.rds")
+T17_2_gfblup_variances_all_5001_6000=readRDS(file="T17_2_gfblup_variances_all_5001_6000.rds")
+T17_2_gfblup_variances_all_6001_7297=readRDS(file="T17_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T17_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_2_gfblup_variances_all=rep(list(list()),cycles)
+T17_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_1_1000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_1001_2000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_2001_3000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_3001_4000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_4001_5000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_5001_6000[[r]])
+	T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_6001_7297[[r]])
+
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_1_1000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_1001_2000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_2001_3000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_3001_4000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_4001_5000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_5001_6000[[r]])
+	T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T17_2_gfblup_prediction_all,"T17_2_gfblup_prediction_all.rds")
+saveRDS(T17_2_gfblup_variances_all,"T17_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_3_gblup_prediction_all_1_1000=readRDS(file="T17_3_gblup_prediction_all_1_1000.rds")
+T17_3_gblup_prediction_all_1001_2000=readRDS(file="T17_3_gblup_prediction_all_1001_2000.rds")
+T17_3_gblup_prediction_all_2001_3000=readRDS(file="T17_3_gblup_prediction_all_2001_3000.rds")
+T17_3_gblup_prediction_all_3001_4000=readRDS(file="T17_3_gblup_prediction_all_3001_4000.rds")
+T17_3_gblup_prediction_all_4001_5000=readRDS(file="T17_3_gblup_prediction_all_4001_5000.rds")
+T17_3_gblup_prediction_all_5001_6000=readRDS(file="T17_3_gblup_prediction_all_5001_6000.rds")
+T17_3_gblup_prediction_all_6001_7297=readRDS(file="T17_3_gblup_prediction_all_6001_7297.rds")
+T17_3_gblup_prediction_all=c(T17_3_gblup_prediction_all_1_1000,T17_3_gblup_prediction_all_1001_2000,T17_3_gblup_prediction_all_2001_3000,T17_3_gblup_prediction_all_3001_4000,T17_3_gblup_prediction_all_4001_5000,T17_3_gblup_prediction_all_5001_6000,T17_3_gblup_prediction_all_6001_7297)
+
+T17_3_gblup_variances_all_1_1000=readRDS(file="T17_3_gblup_variances_all_1_1000.rds")
+T17_3_gblup_variances_all_1001_2000=readRDS(file="T17_3_gblup_variances_all_1001_2000.rds")
+T17_3_gblup_variances_all_2001_3000=readRDS(file="T17_3_gblup_variances_all_2001_3000.rds")
+T17_3_gblup_variances_all_3001_4000=readRDS(file="T17_3_gblup_variances_all_3001_4000.rds")
+T17_3_gblup_variances_all_4001_5000=readRDS(file="T17_3_gblup_variances_all_4001_5000.rds")
+T17_3_gblup_variances_all_5001_6000=readRDS(file="T17_3_gblup_variances_all_5001_6000.rds")
+T17_3_gblup_variances_all_6001_7297=readRDS(file="T17_3_gblup_variances_all_6001_7297.rds")
+T17_3_gblup_variances_all=c(T17_3_gblup_variances_all_1_1000,T17_3_gblup_variances_all_1001_2000,T17_3_gblup_variances_all_2001_3000,T17_3_gblup_variances_all_3001_4000,T17_3_gblup_variances_all_4001_5000,T17_3_gblup_variances_all_5001_6000,T17_3_gblup_variances_all_6001_7297)
+
+saveRDS(T17_3_gblup_prediction_all,"T17_3_gblup_prediction_all.rds")
+saveRDS(T17_3_gblup_variances_all,"T17_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_3_gfblup_prediction_all_1_1000=readRDS(file="T17_3_gfblup_prediction_all_1_1000.rds")
+T17_3_gfblup_prediction_all_1001_2000=readRDS(file="T17_3_gfblup_prediction_all_1001_2000.rds")
+T17_3_gfblup_prediction_all_2001_3000=readRDS(file="T17_3_gfblup_prediction_all_2001_3000.rds")
+T17_3_gfblup_prediction_all_3001_4000=readRDS(file="T17_3_gfblup_prediction_all_3001_4000.rds")
+T17_3_gfblup_prediction_all_4001_5000=readRDS(file="T17_3_gfblup_prediction_all_4001_5000.rds")
+T17_3_gfblup_prediction_all_5001_6000=readRDS(file="T17_3_gfblup_prediction_all_5001_6000.rds")
+T17_3_gfblup_prediction_all_6001_7297=readRDS(file="T17_3_gfblup_prediction_all_6001_7297.rds")
+
+T17_3_gfblup_variances_all_1_1000=readRDS(file="T17_3_gfblup_variances_all_1_1000.rds")
+T17_3_gfblup_variances_all_1001_2000=readRDS(file="T17_3_gfblup_variances_all_1001_2000.rds")
+T17_3_gfblup_variances_all_2001_3000=readRDS(file="T17_3_gfblup_variances_all_2001_3000.rds")
+T17_3_gfblup_variances_all_3001_4000=readRDS(file="T17_3_gfblup_variances_all_3001_4000.rds")
+T17_3_gfblup_variances_all_4001_5000=readRDS(file="T17_3_gfblup_variances_all_4001_5000.rds")
+T17_3_gfblup_variances_all_5001_6000=readRDS(file="T17_3_gfblup_variances_all_5001_6000.rds")
+T17_3_gfblup_variances_all_6001_7297=readRDS(file="T17_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T17_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_3_gfblup_variances_all=rep(list(list()),cycles)
+T17_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_1_1000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_1001_2000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_2001_3000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_3001_4000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_4001_5000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_5001_6000[[r]])
+	T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_6001_7297[[r]])
+
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_1_1000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_1001_2000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_2001_3000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_3001_4000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_4001_5000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_5001_6000[[r]])
+	T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T17_3_gfblup_prediction_all,"T17_3_gfblup_prediction_all.rds")
+saveRDS(T17_3_gfblup_variances_all,"T17_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_4_gblup_prediction_all_1_1000=readRDS(file="T17_4_gblup_prediction_all_1_1000.rds")
+T17_4_gblup_prediction_all_1001_2000=readRDS(file="T17_4_gblup_prediction_all_1001_2000.rds")
+T17_4_gblup_prediction_all_2001_3000=readRDS(file="T17_4_gblup_prediction_all_2001_3000.rds")
+T17_4_gblup_prediction_all_3001_4000=readRDS(file="T17_4_gblup_prediction_all_3001_4000.rds")
+T17_4_gblup_prediction_all_4001_5000=readRDS(file="T17_4_gblup_prediction_all_4001_5000.rds")
+T17_4_gblup_prediction_all_5001_6000=readRDS(file="T17_4_gblup_prediction_all_5001_6000.rds")
+T17_4_gblup_prediction_all_6001_7297=readRDS(file="T17_4_gblup_prediction_all_6001_7297.rds")
+T17_4_gblup_prediction_all=c(T17_4_gblup_prediction_all_1_1000,T17_4_gblup_prediction_all_1001_2000,T17_4_gblup_prediction_all_2001_3000,T17_4_gblup_prediction_all_3001_4000,T17_4_gblup_prediction_all_4001_5000,T17_4_gblup_prediction_all_5001_6000,T17_4_gblup_prediction_all_6001_7297)
+
+T17_4_gblup_variances_all_1_1000=readRDS(file="T17_4_gblup_variances_all_1_1000.rds")
+T17_4_gblup_variances_all_1001_2000=readRDS(file="T17_4_gblup_variances_all_1001_2000.rds")
+T17_4_gblup_variances_all_2001_3000=readRDS(file="T17_4_gblup_variances_all_2001_3000.rds")
+T17_4_gblup_variances_all_3001_4000=readRDS(file="T17_4_gblup_variances_all_3001_4000.rds")
+T17_4_gblup_variances_all_4001_5000=readRDS(file="T17_4_gblup_variances_all_4001_5000.rds")
+T17_4_gblup_variances_all_5001_6000=readRDS(file="T17_4_gblup_variances_all_5001_6000.rds")
+T17_4_gblup_variances_all_6001_7297=readRDS(file="T17_4_gblup_variances_all_6001_7297.rds")
+T17_4_gblup_variances_all=c(T17_4_gblup_variances_all_1_1000,T17_4_gblup_variances_all_1001_2000,T17_4_gblup_variances_all_2001_3000,T17_4_gblup_variances_all_3001_4000,T17_4_gblup_variances_all_4001_5000,T17_4_gblup_variances_all_5001_6000,T17_4_gblup_variances_all_6001_7297)
+
+saveRDS(T17_4_gblup_prediction_all,"T17_4_gblup_prediction_all.rds")
+saveRDS(T17_4_gblup_variances_all,"T17_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_4_gfblup_prediction_all_1_1000=readRDS(file="T17_4_gfblup_prediction_all_1_1000.rds")
+T17_4_gfblup_prediction_all_1001_2000=readRDS(file="T17_4_gfblup_prediction_all_1001_2000.rds")
+T17_4_gfblup_prediction_all_2001_3000=readRDS(file="T17_4_gfblup_prediction_all_2001_3000.rds")
+T17_4_gfblup_prediction_all_3001_4000=readRDS(file="T17_4_gfblup_prediction_all_3001_4000.rds")
+T17_4_gfblup_prediction_all_4001_5000=readRDS(file="T17_4_gfblup_prediction_all_4001_5000.rds")
+T17_4_gfblup_prediction_all_5001_6000=readRDS(file="T17_4_gfblup_prediction_all_5001_6000.rds")
+T17_4_gfblup_prediction_all_6001_7297=readRDS(file="T17_4_gfblup_prediction_all_6001_7297.rds")
+
+T17_4_gfblup_variances_all_1_1000=readRDS(file="T17_4_gfblup_variances_all_1_1000.rds")
+T17_4_gfblup_variances_all_1001_2000=readRDS(file="T17_4_gfblup_variances_all_1001_2000.rds")
+T17_4_gfblup_variances_all_2001_3000=readRDS(file="T17_4_gfblup_variances_all_2001_3000.rds")
+T17_4_gfblup_variances_all_3001_4000=readRDS(file="T17_4_gfblup_variances_all_3001_4000.rds")
+T17_4_gfblup_variances_all_4001_5000=readRDS(file="T17_4_gfblup_variances_all_4001_5000.rds")
+T17_4_gfblup_variances_all_5001_6000=readRDS(file="T17_4_gfblup_variances_all_5001_6000.rds")
+T17_4_gfblup_variances_all_6001_7297=readRDS(file="T17_4_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T17_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_4_gfblup_variances_all=rep(list(list()),cycles)
+T17_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_1_1000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_1001_2000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_2001_3000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_3001_4000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_4001_5000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_5001_6000[[r]])
+	T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_6001_7297[[r]])
+
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_1_1000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_1001_2000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_2001_3000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_3001_4000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_4001_5000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_5001_6000[[r]])
+	T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T17_4_gfblup_prediction_all,"T17_4_gfblup_prediction_all.rds")
+saveRDS(T17_4_gfblup_variances_all,"T17_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_5_gblup_prediction_all_1_1000=readRDS(file="T17_5_gblup_prediction_all_1_1000.rds")
+T17_5_gblup_prediction_all_1001_2000=readRDS(file="T17_5_gblup_prediction_all_1001_2000.rds")
+T17_5_gblup_prediction_all_2001_3000=readRDS(file="T17_5_gblup_prediction_all_2001_3000.rds")
+T17_5_gblup_prediction_all_3001_4000=readRDS(file="T17_5_gblup_prediction_all_3001_4000.rds")
+T17_5_gblup_prediction_all_4001_5000=readRDS(file="T17_5_gblup_prediction_all_4001_5000.rds")
+T17_5_gblup_prediction_all_5001_6000=readRDS(file="T17_5_gblup_prediction_all_5001_6000.rds")
+T17_5_gblup_prediction_all_6001_7297=readRDS(file="T17_5_gblup_prediction_all_6001_7297.rds")
+T17_5_gblup_prediction_all=c(T17_5_gblup_prediction_all_1_1000,T17_5_gblup_prediction_all_1001_2000,T17_5_gblup_prediction_all_2001_3000,T17_5_gblup_prediction_all_3001_4000,T17_5_gblup_prediction_all_4001_5000,T17_5_gblup_prediction_all_5001_6000,T17_5_gblup_prediction_all_6001_7297)
+
+T17_5_gblup_variances_all_1_1000=readRDS(file="T17_5_gblup_variances_all_1_1000.rds")
+T17_5_gblup_variances_all_1001_2000=readRDS(file="T17_5_gblup_variances_all_1001_2000.rds")
+T17_5_gblup_variances_all_2001_3000=readRDS(file="T17_5_gblup_variances_all_2001_3000.rds")
+T17_5_gblup_variances_all_3001_4000=readRDS(file="T17_5_gblup_variances_all_3001_4000.rds")
+T17_5_gblup_variances_all_4001_5000=readRDS(file="T17_5_gblup_variances_all_4001_5000.rds")
+T17_5_gblup_variances_all_5001_6000=readRDS(file="T17_5_gblup_variances_all_5001_6000.rds")
+T17_5_gblup_variances_all_6001_7297=readRDS(file="T17_5_gblup_variances_all_6001_7297.rds")
+T17_5_gblup_variances_all=c(T17_5_gblup_variances_all_1_1000,T17_5_gblup_variances_all_1001_2000,T17_5_gblup_variances_all_2001_3000,T17_5_gblup_variances_all_3001_4000,T17_5_gblup_variances_all_4001_5000,T17_5_gblup_variances_all_5001_6000,T17_5_gblup_variances_all_6001_7297)
+
+saveRDS(T17_5_gblup_prediction_all,"T17_5_gblup_prediction_all.rds")
+saveRDS(T17_5_gblup_variances_all,"T17_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_5_gfblup_prediction_all_1_1000=readRDS(file="T17_5_gfblup_prediction_all_1_1000.rds")
+T17_5_gfblup_prediction_all_1001_2000=readRDS(file="T17_5_gfblup_prediction_all_1001_2000.rds")
+T17_5_gfblup_prediction_all_2001_3000=readRDS(file="T17_5_gfblup_prediction_all_2001_3000.rds")
+T17_5_gfblup_prediction_all_3001_4000=readRDS(file="T17_5_gfblup_prediction_all_3001_4000.rds")
+T17_5_gfblup_prediction_all_4001_5000=readRDS(file="T17_5_gfblup_prediction_all_4001_5000.rds")
+T17_5_gfblup_prediction_all_5001_6000=readRDS(file="T17_5_gfblup_prediction_all_5001_6000.rds")
+T17_5_gfblup_prediction_all_6001_7297=readRDS(file="T17_5_gfblup_prediction_all_6001_7297.rds")
+
+T17_5_gfblup_variances_all_1_1000=readRDS(file="T17_5_gfblup_variances_all_1_1000.rds")
+T17_5_gfblup_variances_all_1001_2000=readRDS(file="T17_5_gfblup_variances_all_1001_2000.rds")
+T17_5_gfblup_variances_all_2001_3000=readRDS(file="T17_5_gfblup_variances_all_2001_3000.rds")
+T17_5_gfblup_variances_all_3001_4000=readRDS(file="T17_5_gfblup_variances_all_3001_4000.rds")
+T17_5_gfblup_variances_all_4001_5000=readRDS(file="T17_5_gfblup_variances_all_4001_5000.rds")
+T17_5_gfblup_variances_all_5001_6000=readRDS(file="T17_5_gfblup_variances_all_5001_6000.rds")
+T17_5_gfblup_variances_all_6001_7297=readRDS(file="T17_5_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T17_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_5_gfblup_variances_all=rep(list(list()),cycles)
+T17_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_1_1000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_1001_2000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_2001_3000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_3001_4000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_4001_5000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_5001_6000[[r]])
+	T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_6001_7297[[r]])
+
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_1_1000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_1001_2000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_2001_3000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_3001_4000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_4001_5000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_5001_6000[[r]])
+	T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T17_5_gfblup_prediction_all,"T17_5_gfblup_prediction_all.rds")
+saveRDS(T17_5_gfblup_variances_all,"T17_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_6_gblup_prediction_all_1_1000=readRDS(file="T17_6_gblup_prediction_all_1_1000.rds")
+T17_6_gblup_prediction_all_1001_2000=readRDS(file="T17_6_gblup_prediction_all_1001_2000.rds")
+T17_6_gblup_prediction_all_2001_3000=readRDS(file="T17_6_gblup_prediction_all_2001_3000.rds")
+T17_6_gblup_prediction_all_3001_4000=readRDS(file="T17_6_gblup_prediction_all_3001_4000.rds")
+T17_6_gblup_prediction_all_4001_5000=readRDS(file="T17_6_gblup_prediction_all_4001_5000.rds")
+T17_6_gblup_prediction_all_5001_6000=readRDS(file="T17_6_gblup_prediction_all_5001_6000.rds")
+T17_6_gblup_prediction_all_6001_7297=readRDS(file="T17_6_gblup_prediction_all_6001_7297.rds")
+T17_6_gblup_prediction_all=c(T17_6_gblup_prediction_all_1_1000,T17_6_gblup_prediction_all_1001_2000,T17_6_gblup_prediction_all_2001_3000,T17_6_gblup_prediction_all_3001_4000,T17_6_gblup_prediction_all_4001_5000,T17_6_gblup_prediction_all_5001_6000,T17_6_gblup_prediction_all_6001_7297)
+
+T17_6_gblup_variances_all_1_1000=readRDS(file="T17_6_gblup_variances_all_1_1000.rds")
+T17_6_gblup_variances_all_1001_2000=readRDS(file="T17_6_gblup_variances_all_1001_2000.rds")
+T17_6_gblup_variances_all_2001_3000=readRDS(file="T17_6_gblup_variances_all_2001_3000.rds")
+T17_6_gblup_variances_all_3001_4000=readRDS(file="T17_6_gblup_variances_all_3001_4000.rds")
+T17_6_gblup_variances_all_4001_5000=readRDS(file="T17_6_gblup_variances_all_4001_5000.rds")
+T17_6_gblup_variances_all_5001_6000=readRDS(file="T17_6_gblup_variances_all_5001_6000.rds")
+T17_6_gblup_variances_all_6001_7297=readRDS(file="T17_6_gblup_variances_all_6001_7297.rds")
+T17_6_gblup_variances_all=c(T17_6_gblup_variances_all_1_1000,T17_6_gblup_variances_all_1001_2000,T17_6_gblup_variances_all_2001_3000,T17_6_gblup_variances_all_3001_4000,T17_6_gblup_variances_all_4001_5000,T17_6_gblup_variances_all_5001_6000,T17_6_gblup_variances_all_6001_7297)
+
+saveRDS(T17_6_gblup_prediction_all,"T17_6_gblup_prediction_all.rds")
+saveRDS(T17_6_gblup_variances_all,"T17_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_6_gfblup_prediction_all_1_1000=readRDS(file="T17_6_gfblup_prediction_all_1_1000.rds")
+T17_6_gfblup_prediction_all_1001_2000=readRDS(file="T17_6_gfblup_prediction_all_1001_2000.rds")
+T17_6_gfblup_prediction_all_2001_3000=readRDS(file="T17_6_gfblup_prediction_all_2001_3000.rds")
+T17_6_gfblup_prediction_all_3001_4000=readRDS(file="T17_6_gfblup_prediction_all_3001_4000.rds")
+T17_6_gfblup_prediction_all_4001_5000=readRDS(file="T17_6_gfblup_prediction_all_4001_5000.rds")
+T17_6_gfblup_prediction_all_5001_6000=readRDS(file="T17_6_gfblup_prediction_all_5001_6000.rds")
+T17_6_gfblup_prediction_all_6001_7297=readRDS(file="T17_6_gfblup_prediction_all_6001_7297.rds")
+
+T17_6_gfblup_variances_all_1_1000=readRDS(file="T17_6_gfblup_variances_all_1_1000.rds")
+T17_6_gfblup_variances_all_1001_2000=readRDS(file="T17_6_gfblup_variances_all_1001_2000.rds")
+T17_6_gfblup_variances_all_2001_3000=readRDS(file="T17_6_gfblup_variances_all_2001_3000.rds")
+T17_6_gfblup_variances_all_3001_4000=readRDS(file="T17_6_gfblup_variances_all_3001_4000.rds")
+T17_6_gfblup_variances_all_4001_5000=readRDS(file="T17_6_gfblup_variances_all_4001_5000.rds")
+T17_6_gfblup_variances_all_5001_6000=readRDS(file="T17_6_gfblup_variances_all_5001_6000.rds")
+T17_6_gfblup_variances_all_6001_7297=readRDS(file="T17_6_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T17_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_6_gfblup_variances_all=rep(list(list()),cycles)
+T17_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_1_1000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_1001_2000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_2001_3000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_3001_4000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_4001_5000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_5001_6000[[r]])
+	T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_6001_7297[[r]])
+
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_1_1000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_1001_2000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_2001_3000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_3001_4000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_4001_5000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_5001_6000[[r]])
+	T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T17_6_gfblup_prediction_all,"T17_6_gfblup_prediction_all.rds")
+saveRDS(T17_6_gfblup_variances_all,"T17_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_7_gblup_prediction_all_1_1000=readRDS(file="T17_7_gblup_prediction_all_1_1000.rds")
+T17_7_gblup_prediction_all_1001_2000=readRDS(file="T17_7_gblup_prediction_all_1001_2000.rds")
+T17_7_gblup_prediction_all_2001_3000=readRDS(file="T17_7_gblup_prediction_all_2001_3000.rds")
+T17_7_gblup_prediction_all_3001_4000=readRDS(file="T17_7_gblup_prediction_all_3001_4000.rds")
+T17_7_gblup_prediction_all_4001_5000=readRDS(file="T17_7_gblup_prediction_all_4001_5000.rds")
+T17_7_gblup_prediction_all_5001_6000=readRDS(file="T17_7_gblup_prediction_all_5001_6000.rds")
+T17_7_gblup_prediction_all_6001_7297=readRDS(file="T17_7_gblup_prediction_all_6001_7297.rds")
+T17_7_gblup_prediction_all=c(T17_7_gblup_prediction_all_1_1000,T17_7_gblup_prediction_all_1001_2000,T17_7_gblup_prediction_all_2001_3000,T17_7_gblup_prediction_all_3001_4000,T17_7_gblup_prediction_all_4001_5000,T17_7_gblup_prediction_all_5001_6000,T17_7_gblup_prediction_all_6001_7297)
+
+T17_7_gblup_variances_all_1_1000=readRDS(file="T17_7_gblup_variances_all_1_1000.rds")
+T17_7_gblup_variances_all_1001_2000=readRDS(file="T17_7_gblup_variances_all_1001_2000.rds")
+T17_7_gblup_variances_all_2001_3000=readRDS(file="T17_7_gblup_variances_all_2001_3000.rds")
+T17_7_gblup_variances_all_3001_4000=readRDS(file="T17_7_gblup_variances_all_3001_4000.rds")
+T17_7_gblup_variances_all_4001_5000=readRDS(file="T17_7_gblup_variances_all_4001_5000.rds")
+T17_7_gblup_variances_all_5001_6000=readRDS(file="T17_7_gblup_variances_all_5001_6000.rds")
+T17_7_gblup_variances_all_6001_7297=readRDS(file="T17_7_gblup_variances_all_6001_7297.rds")
+T17_7_gblup_variances_all=c(T17_7_gblup_variances_all_1_1000,T17_7_gblup_variances_all_1001_2000,T17_7_gblup_variances_all_2001_3000,T17_7_gblup_variances_all_3001_4000,T17_7_gblup_variances_all_4001_5000,T17_7_gblup_variances_all_5001_6000,T17_7_gblup_variances_all_6001_7297)
+
+saveRDS(T17_7_gblup_prediction_all,"T17_7_gblup_prediction_all.rds")
+saveRDS(T17_7_gblup_variances_all,"T17_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_7_gfblup_prediction_all_1_1000=readRDS(file="T17_7_gfblup_prediction_all_1_1000.rds")
+T17_7_gfblup_prediction_all_1001_2000=readRDS(file="T17_7_gfblup_prediction_all_1001_2000.rds")
+T17_7_gfblup_prediction_all_2001_3000=readRDS(file="T17_7_gfblup_prediction_all_2001_3000.rds")
+T17_7_gfblup_prediction_all_3001_4000=readRDS(file="T17_7_gfblup_prediction_all_3001_4000.rds")
+T17_7_gfblup_prediction_all_4001_5000=readRDS(file="T17_7_gfblup_prediction_all_4001_5000.rds")
+T17_7_gfblup_prediction_all_5001_6000=readRDS(file="T17_7_gfblup_prediction_all_5001_6000.rds")
+T17_7_gfblup_prediction_all_6001_7297=readRDS(file="T17_7_gfblup_prediction_all_6001_7297.rds")
+
+T17_7_gfblup_variances_all_1_1000=readRDS(file="T17_7_gfblup_variances_all_1_1000.rds")
+T17_7_gfblup_variances_all_1001_2000=readRDS(file="T17_7_gfblup_variances_all_1001_2000.rds")
+T17_7_gfblup_variances_all_2001_3000=readRDS(file="T17_7_gfblup_variances_all_2001_3000.rds")
+T17_7_gfblup_variances_all_3001_4000=readRDS(file="T17_7_gfblup_variances_all_3001_4000.rds")
+T17_7_gfblup_variances_all_4001_5000=readRDS(file="T17_7_gfblup_variances_all_4001_5000.rds")
+T17_7_gfblup_variances_all_5001_6000=readRDS(file="T17_7_gfblup_variances_all_5001_6000.rds")
+T17_7_gfblup_variances_all_6001_7297=readRDS(file="T17_7_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T17_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_7_gfblup_variances_all=rep(list(list()),cycles)
+T17_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_1_1000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_1001_2000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_2001_3000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_3001_4000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_4001_5000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_5001_6000[[r]])
+	T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_6001_7297[[r]])
+
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_1_1000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_1001_2000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_2001_3000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_3001_4000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_4001_5000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_5001_6000[[r]])
+	T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T17_7_gfblup_prediction_all,"T17_7_gfblup_prediction_all.rds")
+saveRDS(T17_7_gfblup_variances_all,"T17_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_8_gblup_prediction_all_1_1000=readRDS(file="T17_8_gblup_prediction_all_1_1000.rds")
+T17_8_gblup_prediction_all_1001_2000=readRDS(file="T17_8_gblup_prediction_all_1001_2000.rds")
+T17_8_gblup_prediction_all_2001_3000=readRDS(file="T17_8_gblup_prediction_all_2001_3000.rds")
+T17_8_gblup_prediction_all_3001_4000=readRDS(file="T17_8_gblup_prediction_all_3001_4000.rds")
+T17_8_gblup_prediction_all_4001_5000=readRDS(file="T17_8_gblup_prediction_all_4001_5000.rds")
+T17_8_gblup_prediction_all_5001_6000=readRDS(file="T17_8_gblup_prediction_all_5001_6000.rds")
+T17_8_gblup_prediction_all_6001_7297=readRDS(file="T17_8_gblup_prediction_all_6001_7297.rds")
+T17_8_gblup_prediction_all=c(T17_8_gblup_prediction_all_1_1000,T17_8_gblup_prediction_all_1001_2000,T17_8_gblup_prediction_all_2001_3000,T17_8_gblup_prediction_all_3001_4000,T17_8_gblup_prediction_all_4001_5000,T17_8_gblup_prediction_all_5001_6000,T17_8_gblup_prediction_all_6001_7297)
+
+T17_8_gblup_variances_all_1_1000=readRDS(file="T17_8_gblup_variances_all_1_1000.rds")
+T17_8_gblup_variances_all_1001_2000=readRDS(file="T17_8_gblup_variances_all_1001_2000.rds")
+T17_8_gblup_variances_all_2001_3000=readRDS(file="T17_8_gblup_variances_all_2001_3000.rds")
+T17_8_gblup_variances_all_3001_4000=readRDS(file="T17_8_gblup_variances_all_3001_4000.rds")
+T17_8_gblup_variances_all_4001_5000=readRDS(file="T17_8_gblup_variances_all_4001_5000.rds")
+T17_8_gblup_variances_all_5001_6000=readRDS(file="T17_8_gblup_variances_all_5001_6000.rds")
+T17_8_gblup_variances_all_6001_7297=readRDS(file="T17_8_gblup_variances_all_6001_7297.rds")
+T17_8_gblup_variances_all=c(T17_8_gblup_variances_all_1_1000,T17_8_gblup_variances_all_1001_2000,T17_8_gblup_variances_all_2001_3000,T17_8_gblup_variances_all_3001_4000,T17_8_gblup_variances_all_4001_5000,T17_8_gblup_variances_all_5001_6000,T17_8_gblup_variances_all_6001_7297)
+
+saveRDS(T17_8_gblup_prediction_all,"T17_8_gblup_prediction_all.rds")
+saveRDS(T17_8_gblup_variances_all,"T17_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T17_8_gfblup_prediction_all_1_1000=readRDS(file="T17_8_gfblup_prediction_all_1_1000.rds")
+T17_8_gfblup_prediction_all_1001_2000=readRDS(file="T17_8_gfblup_prediction_all_1001_2000.rds")
+T17_8_gfblup_prediction_all_2001_3000=readRDS(file="T17_8_gfblup_prediction_all_2001_3000.rds")
+T17_8_gfblup_prediction_all_3001_4000=readRDS(file="T17_8_gfblup_prediction_all_3001_4000.rds")
+T17_8_gfblup_prediction_all_4001_5000=readRDS(file="T17_8_gfblup_prediction_all_4001_5000.rds")
+T17_8_gfblup_prediction_all_5001_6000=readRDS(file="T17_8_gfblup_prediction_all_5001_6000.rds")
+T17_8_gfblup_prediction_all_6001_7297=readRDS(file="T17_8_gfblup_prediction_all_6001_7297.rds")
+
+T17_8_gfblup_variances_all_1_1000=readRDS(file="T17_8_gfblup_variances_all_1_1000.rds")
+T17_8_gfblup_variances_all_1001_2000=readRDS(file="T17_8_gfblup_variances_all_1001_2000.rds")
+T17_8_gfblup_variances_all_2001_3000=readRDS(file="T17_8_gfblup_variances_all_2001_3000.rds")
+T17_8_gfblup_variances_all_3001_4000=readRDS(file="T17_8_gfblup_variances_all_3001_4000.rds")
+T17_8_gfblup_variances_all_4001_5000=readRDS(file="T17_8_gfblup_variances_all_4001_5000.rds")
+T17_8_gfblup_variances_all_5001_6000=readRDS(file="T17_8_gfblup_variances_all_5001_6000.rds")
+T17_8_gfblup_variances_all_6001_7297=readRDS(file="T17_8_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T17_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T17_8_gfblup_variances_all=rep(list(list()),cycles)
+T17_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_1_1000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_1001_2000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_2001_3000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_3001_4000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_4001_5000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_5001_6000[[r]])
+	T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_6001_7297[[r]])
+
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_1_1000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_1001_2000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_2001_3000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_3001_4000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_4001_5000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_5001_6000[[r]])
+	T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T17_8_gfblup_prediction_all,"T17_8_gfblup_prediction_all.rds")
+saveRDS(T17_8_gfblup_variances_all,"T17_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_1_gblup_prediction_all_1_1000=readRDS(file="T18_1_gblup_prediction_all_1_1000.rds")
+T18_1_gblup_prediction_all_1001_2000=readRDS(file="T18_1_gblup_prediction_all_1001_2000.rds")
+T18_1_gblup_prediction_all_2001_3000=readRDS(file="T18_1_gblup_prediction_all_2001_3000.rds")
+T18_1_gblup_prediction_all_3001_4000=readRDS(file="T18_1_gblup_prediction_all_3001_4000.rds")
+T18_1_gblup_prediction_all_4001_5000=readRDS(file="T18_1_gblup_prediction_all_4001_5000.rds")
+T18_1_gblup_prediction_all_5001_6000=readRDS(file="T18_1_gblup_prediction_all_5001_6000.rds")
+T18_1_gblup_prediction_all_6001_7297=readRDS(file="T18_1_gblup_prediction_all_6001_7297.rds")
+T18_1_gblup_prediction_all=c(T18_1_gblup_prediction_all_1_1000,T18_1_gblup_prediction_all_1001_2000,T18_1_gblup_prediction_all_2001_3000,T18_1_gblup_prediction_all_3001_4000,T18_1_gblup_prediction_all_4001_5000,T18_1_gblup_prediction_all_5001_6000,T18_1_gblup_prediction_all_6001_7297)
+
+T18_1_gblup_variances_all_1_1000=readRDS(file="T18_1_gblup_variances_all_1_1000.rds")
+T18_1_gblup_variances_all_1001_2000=readRDS(file="T18_1_gblup_variances_all_1001_2000.rds")
+T18_1_gblup_variances_all_2001_3000=readRDS(file="T18_1_gblup_variances_all_2001_3000.rds")
+T18_1_gblup_variances_all_3001_4000=readRDS(file="T18_1_gblup_variances_all_3001_4000.rds")
+T18_1_gblup_variances_all_4001_5000=readRDS(file="T18_1_gblup_variances_all_4001_5000.rds")
+T18_1_gblup_variances_all_5001_6000=readRDS(file="T18_1_gblup_variances_all_5001_6000.rds")
+T18_1_gblup_variances_all_6001_7297=readRDS(file="T18_1_gblup_variances_all_6001_7297.rds")
+T18_1_gblup_variances_all=c(T18_1_gblup_variances_all_1_1000,T18_1_gblup_variances_all_1001_2000,T18_1_gblup_variances_all_2001_3000,T18_1_gblup_variances_all_3001_4000,T18_1_gblup_variances_all_4001_5000,T18_1_gblup_variances_all_5001_6000,T18_1_gblup_variances_all_6001_7297)
+
+saveRDS(T18_1_gblup_prediction_all,"T18_1_gblup_prediction_all.rds")
+saveRDS(T18_1_gblup_variances_all,"T18_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_1_gfblup_prediction_all_1_1000=readRDS(file="T18_1_gfblup_prediction_all_1_1000.rds")
+T18_1_gfblup_prediction_all_1001_2000=readRDS(file="T18_1_gfblup_prediction_all_1001_2000.rds")
+T18_1_gfblup_prediction_all_2001_3000=readRDS(file="T18_1_gfblup_prediction_all_2001_3000.rds")
+T18_1_gfblup_prediction_all_3001_4000=readRDS(file="T18_1_gfblup_prediction_all_3001_4000.rds")
+T18_1_gfblup_prediction_all_4001_5000=readRDS(file="T18_1_gfblup_prediction_all_4001_5000.rds")
+T18_1_gfblup_prediction_all_5001_6000=readRDS(file="T18_1_gfblup_prediction_all_5001_6000.rds")
+T18_1_gfblup_prediction_all_6001_7297=readRDS(file="T18_1_gfblup_prediction_all_6001_7297.rds")
+
+T18_1_gfblup_variances_all_1_1000=readRDS(file="T18_1_gfblup_variances_all_1_1000.rds")
+T18_1_gfblup_variances_all_1001_2000=readRDS(file="T18_1_gfblup_variances_all_1001_2000.rds")
+T18_1_gfblup_variances_all_2001_3000=readRDS(file="T18_1_gfblup_variances_all_2001_3000.rds")
+T18_1_gfblup_variances_all_3001_4000=readRDS(file="T18_1_gfblup_variances_all_3001_4000.rds")
+T18_1_gfblup_variances_all_4001_5000=readRDS(file="T18_1_gfblup_variances_all_4001_5000.rds")
+T18_1_gfblup_variances_all_5001_6000=readRDS(file="T18_1_gfblup_variances_all_5001_6000.rds")
+T18_1_gfblup_variances_all_6001_7297=readRDS(file="T18_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T18_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_1_gfblup_variances_all=rep(list(list()),cycles)
+T18_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_1_1000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_1001_2000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_2001_3000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_3001_4000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_4001_5000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_5001_6000[[r]])
+	T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_6001_7297[[r]])
+
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_1_1000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_1001_2000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_2001_3000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_3001_4000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_4001_5000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_5001_6000[[r]])
+	T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T18_1_gfblup_prediction_all,"T18_1_gfblup_prediction_all.rds")
+saveRDS(T18_1_gfblup_variances_all,"T18_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_2_gblup_prediction_all_1_1000=readRDS(file="T18_2_gblup_prediction_all_1_1000.rds")
+T18_2_gblup_prediction_all_1001_2000=readRDS(file="T18_2_gblup_prediction_all_1001_2000.rds")
+T18_2_gblup_prediction_all_2001_3000=readRDS(file="T18_2_gblup_prediction_all_2001_3000.rds")
+T18_2_gblup_prediction_all_3001_4000=readRDS(file="T18_2_gblup_prediction_all_3001_4000.rds")
+T18_2_gblup_prediction_all_4001_5000=readRDS(file="T18_2_gblup_prediction_all_4001_5000.rds")
+T18_2_gblup_prediction_all_5001_6000=readRDS(file="T18_2_gblup_prediction_all_5001_6000.rds")
+T18_2_gblup_prediction_all_6001_7297=readRDS(file="T18_2_gblup_prediction_all_6001_7297.rds")
+T18_2_gblup_prediction_all=c(T18_2_gblup_prediction_all_1_1000,T18_2_gblup_prediction_all_1001_2000,T18_2_gblup_prediction_all_2001_3000,T18_2_gblup_prediction_all_3001_4000,T18_2_gblup_prediction_all_4001_5000,T18_2_gblup_prediction_all_5001_6000,T18_2_gblup_prediction_all_6001_7297)
+
+T18_2_gblup_variances_all_1_1000=readRDS(file="T18_2_gblup_variances_all_1_1000.rds")
+T18_2_gblup_variances_all_1001_2000=readRDS(file="T18_2_gblup_variances_all_1001_2000.rds")
+T18_2_gblup_variances_all_2001_3000=readRDS(file="T18_2_gblup_variances_all_2001_3000.rds")
+T18_2_gblup_variances_all_3001_4000=readRDS(file="T18_2_gblup_variances_all_3001_4000.rds")
+T18_2_gblup_variances_all_4001_5000=readRDS(file="T18_2_gblup_variances_all_4001_5000.rds")
+T18_2_gblup_variances_all_5001_6000=readRDS(file="T18_2_gblup_variances_all_5001_6000.rds")
+T18_2_gblup_variances_all_6001_7297=readRDS(file="T18_2_gblup_variances_all_6001_7297.rds")
+T18_2_gblup_variances_all=c(T18_2_gblup_variances_all_1_1000,T18_2_gblup_variances_all_1001_2000,T18_2_gblup_variances_all_2001_3000,T18_2_gblup_variances_all_3001_4000,T18_2_gblup_variances_all_4001_5000,T18_2_gblup_variances_all_5001_6000,T18_2_gblup_variances_all_6001_7297)
+
+saveRDS(T18_2_gblup_prediction_all,"T18_2_gblup_prediction_all.rds")
+saveRDS(T18_2_gblup_variances_all,"T18_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_2_gfblup_prediction_all_1_1000=readRDS(file="T18_2_gfblup_prediction_all_1_1000.rds")
+T18_2_gfblup_prediction_all_1001_2000=readRDS(file="T18_2_gfblup_prediction_all_1001_2000.rds")
+T18_2_gfblup_prediction_all_2001_3000=readRDS(file="T18_2_gfblup_prediction_all_2001_3000.rds")
+T18_2_gfblup_prediction_all_3001_4000=readRDS(file="T18_2_gfblup_prediction_all_3001_4000.rds")
+T18_2_gfblup_prediction_all_4001_5000=readRDS(file="T18_2_gfblup_prediction_all_4001_5000.rds")
+T18_2_gfblup_prediction_all_5001_6000=readRDS(file="T18_2_gfblup_prediction_all_5001_6000.rds")
+T18_2_gfblup_prediction_all_6001_7297=readRDS(file="T18_2_gfblup_prediction_all_6001_7297.rds")
+
+T18_2_gfblup_variances_all_1_1000=readRDS(file="T18_2_gfblup_variances_all_1_1000.rds")
+T18_2_gfblup_variances_all_1001_2000=readRDS(file="T18_2_gfblup_variances_all_1001_2000.rds")
+T18_2_gfblup_variances_all_2001_3000=readRDS(file="T18_2_gfblup_variances_all_2001_3000.rds")
+T18_2_gfblup_variances_all_3001_4000=readRDS(file="T18_2_gfblup_variances_all_3001_4000.rds")
+T18_2_gfblup_variances_all_4001_5000=readRDS(file="T18_2_gfblup_variances_all_4001_5000.rds")
+T18_2_gfblup_variances_all_5001_6000=readRDS(file="T18_2_gfblup_variances_all_5001_6000.rds")
+T18_2_gfblup_variances_all_6001_7297=readRDS(file="T18_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T18_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_2_gfblup_variances_all=rep(list(list()),cycles)
+T18_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_1_1000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_1001_2000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_2001_3000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_3001_4000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_4001_5000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_5001_6000[[r]])
+	T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_6001_7297[[r]])
+
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_1_1000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_1001_2000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_2001_3000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_3001_4000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_4001_5000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_5001_6000[[r]])
+	T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T18_2_gfblup_prediction_all,"T18_2_gfblup_prediction_all.rds")
+saveRDS(T18_2_gfblup_variances_all,"T18_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_3_gblup_prediction_all_1_1000=readRDS(file="T18_3_gblup_prediction_all_1_1000.rds")
+T18_3_gblup_prediction_all_1001_2000=readRDS(file="T18_3_gblup_prediction_all_1001_2000.rds")
+T18_3_gblup_prediction_all_2001_3000=readRDS(file="T18_3_gblup_prediction_all_2001_3000.rds")
+T18_3_gblup_prediction_all_3001_4000=readRDS(file="T18_3_gblup_prediction_all_3001_4000.rds")
+T18_3_gblup_prediction_all_4001_5000=readRDS(file="T18_3_gblup_prediction_all_4001_5000.rds")
+T18_3_gblup_prediction_all_5001_6000=readRDS(file="T18_3_gblup_prediction_all_5001_6000.rds")
+T18_3_gblup_prediction_all_6001_7297=readRDS(file="T18_3_gblup_prediction_all_6001_7297.rds")
+T18_3_gblup_prediction_all=c(T18_3_gblup_prediction_all_1_1000,T18_3_gblup_prediction_all_1001_2000,T18_3_gblup_prediction_all_2001_3000,T18_3_gblup_prediction_all_3001_4000,T18_3_gblup_prediction_all_4001_5000,T18_3_gblup_prediction_all_5001_6000,T18_3_gblup_prediction_all_6001_7297)
+
+T18_3_gblup_variances_all_1_1000=readRDS(file="T18_3_gblup_variances_all_1_1000.rds")
+T18_3_gblup_variances_all_1001_2000=readRDS(file="T18_3_gblup_variances_all_1001_2000.rds")
+T18_3_gblup_variances_all_2001_3000=readRDS(file="T18_3_gblup_variances_all_2001_3000.rds")
+T18_3_gblup_variances_all_3001_4000=readRDS(file="T18_3_gblup_variances_all_3001_4000.rds")
+T18_3_gblup_variances_all_4001_5000=readRDS(file="T18_3_gblup_variances_all_4001_5000.rds")
+T18_3_gblup_variances_all_5001_6000=readRDS(file="T18_3_gblup_variances_all_5001_6000.rds")
+T18_3_gblup_variances_all_6001_7297=readRDS(file="T18_3_gblup_variances_all_6001_7297.rds")
+T18_3_gblup_variances_all=c(T18_3_gblup_variances_all_1_1000,T18_3_gblup_variances_all_1001_2000,T18_3_gblup_variances_all_2001_3000,T18_3_gblup_variances_all_3001_4000,T18_3_gblup_variances_all_4001_5000,T18_3_gblup_variances_all_5001_6000,T18_3_gblup_variances_all_6001_7297)
+
+saveRDS(T18_3_gblup_prediction_all,"T18_3_gblup_prediction_all.rds")
+saveRDS(T18_3_gblup_variances_all,"T18_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_3_gfblup_prediction_all_1_1000=readRDS(file="T18_3_gfblup_prediction_all_1_1000.rds")
+T18_3_gfblup_prediction_all_1001_2000=readRDS(file="T18_3_gfblup_prediction_all_1001_2000.rds")
+T18_3_gfblup_prediction_all_2001_3000=readRDS(file="T18_3_gfblup_prediction_all_2001_3000.rds")
+T18_3_gfblup_prediction_all_3001_4000=readRDS(file="T18_3_gfblup_prediction_all_3001_4000.rds")
+T18_3_gfblup_prediction_all_4001_5000=readRDS(file="T18_3_gfblup_prediction_all_4001_5000.rds")
+T18_3_gfblup_prediction_all_5001_6000=readRDS(file="T18_3_gfblup_prediction_all_5001_6000.rds")
+T18_3_gfblup_prediction_all_6001_7297=readRDS(file="T18_3_gfblup_prediction_all_6001_7297.rds")
+
+T18_3_gfblup_variances_all_1_1000=readRDS(file="T18_3_gfblup_variances_all_1_1000.rds")
+T18_3_gfblup_variances_all_1001_2000=readRDS(file="T18_3_gfblup_variances_all_1001_2000.rds")
+T18_3_gfblup_variances_all_2001_3000=readRDS(file="T18_3_gfblup_variances_all_2001_3000.rds")
+T18_3_gfblup_variances_all_3001_4000=readRDS(file="T18_3_gfblup_variances_all_3001_4000.rds")
+T18_3_gfblup_variances_all_4001_5000=readRDS(file="T18_3_gfblup_variances_all_4001_5000.rds")
+T18_3_gfblup_variances_all_5001_6000=readRDS(file="T18_3_gfblup_variances_all_5001_6000.rds")
+T18_3_gfblup_variances_all_6001_7297=readRDS(file="T18_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T18_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_3_gfblup_variances_all=rep(list(list()),cycles)
+T18_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_1_1000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_1001_2000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_2001_3000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_3001_4000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_4001_5000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_5001_6000[[r]])
+	T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_6001_7297[[r]])
+
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_1_1000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_1001_2000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_2001_3000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_3001_4000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_4001_5000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_5001_6000[[r]])
+	T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T18_3_gfblup_prediction_all,"T18_3_gfblup_prediction_all.rds")
+saveRDS(T18_3_gfblup_variances_all,"T18_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_4_gblup_prediction_all_1_1000=readRDS(file="T18_4_gblup_prediction_all_1_1000.rds")
+T18_4_gblup_prediction_all_1001_2000=readRDS(file="T18_4_gblup_prediction_all_1001_2000.rds")
+T18_4_gblup_prediction_all_2001_3000=readRDS(file="T18_4_gblup_prediction_all_2001_3000.rds")
+T18_4_gblup_prediction_all_3001_4000=readRDS(file="T18_4_gblup_prediction_all_3001_4000.rds")
+T18_4_gblup_prediction_all_4001_5000=readRDS(file="T18_4_gblup_prediction_all_4001_5000.rds")
+T18_4_gblup_prediction_all_5001_6000=readRDS(file="T18_4_gblup_prediction_all_5001_6000.rds")
+T18_4_gblup_prediction_all_6001_7297=readRDS(file="T18_4_gblup_prediction_all_6001_7297.rds")
+T18_4_gblup_prediction_all=c(T18_4_gblup_prediction_all_1_1000,T18_4_gblup_prediction_all_1001_2000,T18_4_gblup_prediction_all_2001_3000,T18_4_gblup_prediction_all_3001_4000,T18_4_gblup_prediction_all_4001_5000,T18_4_gblup_prediction_all_5001_6000,T18_4_gblup_prediction_all_6001_7297)
+
+T18_4_gblup_variances_all_1_1000=readRDS(file="T18_4_gblup_variances_all_1_1000.rds")
+T18_4_gblup_variances_all_1001_2000=readRDS(file="T18_4_gblup_variances_all_1001_2000.rds")
+T18_4_gblup_variances_all_2001_3000=readRDS(file="T18_4_gblup_variances_all_2001_3000.rds")
+T18_4_gblup_variances_all_3001_4000=readRDS(file="T18_4_gblup_variances_all_3001_4000.rds")
+T18_4_gblup_variances_all_4001_5000=readRDS(file="T18_4_gblup_variances_all_4001_5000.rds")
+T18_4_gblup_variances_all_5001_6000=readRDS(file="T18_4_gblup_variances_all_5001_6000.rds")
+T18_4_gblup_variances_all_6001_7297=readRDS(file="T18_4_gblup_variances_all_6001_7297.rds")
+T18_4_gblup_variances_all=c(T18_4_gblup_variances_all_1_1000,T18_4_gblup_variances_all_1001_2000,T18_4_gblup_variances_all_2001_3000,T18_4_gblup_variances_all_3001_4000,T18_4_gblup_variances_all_4001_5000,T18_4_gblup_variances_all_5001_6000,T18_4_gblup_variances_all_6001_7297)
+
+saveRDS(T18_4_gblup_prediction_all,"T18_4_gblup_prediction_all.rds")
+saveRDS(T18_4_gblup_variances_all,"T18_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_4_gfblup_prediction_all_1_1000=readRDS(file="T18_4_gfblup_prediction_all_1_1000.rds")
+T18_4_gfblup_prediction_all_1001_2000=readRDS(file="T18_4_gfblup_prediction_all_1001_2000.rds")
+T18_4_gfblup_prediction_all_2001_3000=readRDS(file="T18_4_gfblup_prediction_all_2001_3000.rds")
+T18_4_gfblup_prediction_all_3001_4000=readRDS(file="T18_4_gfblup_prediction_all_3001_4000.rds")
+T18_4_gfblup_prediction_all_4001_5000=readRDS(file="T18_4_gfblup_prediction_all_4001_5000.rds")
+T18_4_gfblup_prediction_all_5001_6000=readRDS(file="T18_4_gfblup_prediction_all_5001_6000.rds")
+T18_4_gfblup_prediction_all_6001_7297=readRDS(file="T18_4_gfblup_prediction_all_6001_7297.rds")
+
+T18_4_gfblup_variances_all_1_1000=readRDS(file="T18_4_gfblup_variances_all_1_1000.rds")
+T18_4_gfblup_variances_all_1001_2000=readRDS(file="T18_4_gfblup_variances_all_1001_2000.rds")
+T18_4_gfblup_variances_all_2001_3000=readRDS(file="T18_4_gfblup_variances_all_2001_3000.rds")
+T18_4_gfblup_variances_all_3001_4000=readRDS(file="T18_4_gfblup_variances_all_3001_4000.rds")
+T18_4_gfblup_variances_all_4001_5000=readRDS(file="T18_4_gfblup_variances_all_4001_5000.rds")
+T18_4_gfblup_variances_all_5001_6000=readRDS(file="T18_4_gfblup_variances_all_5001_6000.rds")
+T18_4_gfblup_variances_all_6001_7297=readRDS(file="T18_4_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T18_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_4_gfblup_variances_all=rep(list(list()),cycles)
+T18_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_1_1000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_1001_2000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_2001_3000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_3001_4000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_4001_5000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_5001_6000[[r]])
+	T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_6001_7297[[r]])
+
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_1_1000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_1001_2000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_2001_3000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_3001_4000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_4001_5000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_5001_6000[[r]])
+	T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T18_4_gfblup_prediction_all,"T18_4_gfblup_prediction_all.rds")
+saveRDS(T18_4_gfblup_variances_all,"T18_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_5_gblup_prediction_all_1_1000=readRDS(file="T18_5_gblup_prediction_all_1_1000.rds")
+T18_5_gblup_prediction_all_1001_2000=readRDS(file="T18_5_gblup_prediction_all_1001_2000.rds")
+T18_5_gblup_prediction_all_2001_3000=readRDS(file="T18_5_gblup_prediction_all_2001_3000.rds")
+T18_5_gblup_prediction_all_3001_4000=readRDS(file="T18_5_gblup_prediction_all_3001_4000.rds")
+T18_5_gblup_prediction_all_4001_5000=readRDS(file="T18_5_gblup_prediction_all_4001_5000.rds")
+T18_5_gblup_prediction_all_5001_6000=readRDS(file="T18_5_gblup_prediction_all_5001_6000.rds")
+T18_5_gblup_prediction_all_6001_7297=readRDS(file="T18_5_gblup_prediction_all_6001_7297.rds")
+T18_5_gblup_prediction_all=c(T18_5_gblup_prediction_all_1_1000,T18_5_gblup_prediction_all_1001_2000,T18_5_gblup_prediction_all_2001_3000,T18_5_gblup_prediction_all_3001_4000,T18_5_gblup_prediction_all_4001_5000,T18_5_gblup_prediction_all_5001_6000,T18_5_gblup_prediction_all_6001_7297)
+
+T18_5_gblup_variances_all_1_1000=readRDS(file="T18_5_gblup_variances_all_1_1000.rds")
+T18_5_gblup_variances_all_1001_2000=readRDS(file="T18_5_gblup_variances_all_1001_2000.rds")
+T18_5_gblup_variances_all_2001_3000=readRDS(file="T18_5_gblup_variances_all_2001_3000.rds")
+T18_5_gblup_variances_all_3001_4000=readRDS(file="T18_5_gblup_variances_all_3001_4000.rds")
+T18_5_gblup_variances_all_4001_5000=readRDS(file="T18_5_gblup_variances_all_4001_5000.rds")
+T18_5_gblup_variances_all_5001_6000=readRDS(file="T18_5_gblup_variances_all_5001_6000.rds")
+T18_5_gblup_variances_all_6001_7297=readRDS(file="T18_5_gblup_variances_all_6001_7297.rds")
+T18_5_gblup_variances_all=c(T18_5_gblup_variances_all_1_1000,T18_5_gblup_variances_all_1001_2000,T18_5_gblup_variances_all_2001_3000,T18_5_gblup_variances_all_3001_4000,T18_5_gblup_variances_all_4001_5000,T18_5_gblup_variances_all_5001_6000,T18_5_gblup_variances_all_6001_7297)
+
+saveRDS(T18_5_gblup_prediction_all,"T18_5_gblup_prediction_all.rds")
+saveRDS(T18_5_gblup_variances_all,"T18_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_5_gfblup_prediction_all_1_1000=readRDS(file="T18_5_gfblup_prediction_all_1_1000.rds")
+T18_5_gfblup_prediction_all_1001_2000=readRDS(file="T18_5_gfblup_prediction_all_1001_2000.rds")
+T18_5_gfblup_prediction_all_2001_3000=readRDS(file="T18_5_gfblup_prediction_all_2001_3000.rds")
+T18_5_gfblup_prediction_all_3001_4000=readRDS(file="T18_5_gfblup_prediction_all_3001_4000.rds")
+T18_5_gfblup_prediction_all_4001_5000=readRDS(file="T18_5_gfblup_prediction_all_4001_5000.rds")
+T18_5_gfblup_prediction_all_5001_6000=readRDS(file="T18_5_gfblup_prediction_all_5001_6000.rds")
+T18_5_gfblup_prediction_all_6001_7297=readRDS(file="T18_5_gfblup_prediction_all_6001_7297.rds")
+
+T18_5_gfblup_variances_all_1_1000=readRDS(file="T18_5_gfblup_variances_all_1_1000.rds")
+T18_5_gfblup_variances_all_1001_2000=readRDS(file="T18_5_gfblup_variances_all_1001_2000.rds")
+T18_5_gfblup_variances_all_2001_3000=readRDS(file="T18_5_gfblup_variances_all_2001_3000.rds")
+T18_5_gfblup_variances_all_3001_4000=readRDS(file="T18_5_gfblup_variances_all_3001_4000.rds")
+T18_5_gfblup_variances_all_4001_5000=readRDS(file="T18_5_gfblup_variances_all_4001_5000.rds")
+T18_5_gfblup_variances_all_5001_6000=readRDS(file="T18_5_gfblup_variances_all_5001_6000.rds")
+T18_5_gfblup_variances_all_6001_7297=readRDS(file="T18_5_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T18_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_5_gfblup_variances_all=rep(list(list()),cycles)
+T18_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_1_1000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_1001_2000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_2001_3000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_3001_4000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_4001_5000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_5001_6000[[r]])
+	T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_6001_7297[[r]])
+
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_1_1000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_1001_2000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_2001_3000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_3001_4000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_4001_5000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_5001_6000[[r]])
+	T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T18_5_gfblup_prediction_all,"T18_5_gfblup_prediction_all.rds")
+saveRDS(T18_5_gfblup_variances_all,"T18_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_6_gblup_prediction_all_1_1000=readRDS(file="T18_6_gblup_prediction_all_1_1000.rds")
+T18_6_gblup_prediction_all_1001_2000=readRDS(file="T18_6_gblup_prediction_all_1001_2000.rds")
+T18_6_gblup_prediction_all_2001_3000=readRDS(file="T18_6_gblup_prediction_all_2001_3000.rds")
+T18_6_gblup_prediction_all_3001_4000=readRDS(file="T18_6_gblup_prediction_all_3001_4000.rds")
+T18_6_gblup_prediction_all_4001_5000=readRDS(file="T18_6_gblup_prediction_all_4001_5000.rds")
+T18_6_gblup_prediction_all_5001_6000=readRDS(file="T18_6_gblup_prediction_all_5001_6000.rds")
+T18_6_gblup_prediction_all_6001_7297=readRDS(file="T18_6_gblup_prediction_all_6001_7297.rds")
+T18_6_gblup_prediction_all=c(T18_6_gblup_prediction_all_1_1000,T18_6_gblup_prediction_all_1001_2000,T18_6_gblup_prediction_all_2001_3000,T18_6_gblup_prediction_all_3001_4000,T18_6_gblup_prediction_all_4001_5000,T18_6_gblup_prediction_all_5001_6000,T18_6_gblup_prediction_all_6001_7297)
+
+T18_6_gblup_variances_all_1_1000=readRDS(file="T18_6_gblup_variances_all_1_1000.rds")
+T18_6_gblup_variances_all_1001_2000=readRDS(file="T18_6_gblup_variances_all_1001_2000.rds")
+T18_6_gblup_variances_all_2001_3000=readRDS(file="T18_6_gblup_variances_all_2001_3000.rds")
+T18_6_gblup_variances_all_3001_4000=readRDS(file="T18_6_gblup_variances_all_3001_4000.rds")
+T18_6_gblup_variances_all_4001_5000=readRDS(file="T18_6_gblup_variances_all_4001_5000.rds")
+T18_6_gblup_variances_all_5001_6000=readRDS(file="T18_6_gblup_variances_all_5001_6000.rds")
+T18_6_gblup_variances_all_6001_7297=readRDS(file="T18_6_gblup_variances_all_6001_7297.rds")
+T18_6_gblup_variances_all=c(T18_6_gblup_variances_all_1_1000,T18_6_gblup_variances_all_1001_2000,T18_6_gblup_variances_all_2001_3000,T18_6_gblup_variances_all_3001_4000,T18_6_gblup_variances_all_4001_5000,T18_6_gblup_variances_all_5001_6000,T18_6_gblup_variances_all_6001_7297)
+
+saveRDS(T18_6_gblup_prediction_all,"T18_6_gblup_prediction_all.rds")
+saveRDS(T18_6_gblup_variances_all,"T18_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_6_gfblup_prediction_all_1_1000=readRDS(file="T18_6_gfblup_prediction_all_1_1000.rds")
+T18_6_gfblup_prediction_all_1001_2000=readRDS(file="T18_6_gfblup_prediction_all_1001_2000.rds")
+T18_6_gfblup_prediction_all_2001_3000=readRDS(file="T18_6_gfblup_prediction_all_2001_3000.rds")
+T18_6_gfblup_prediction_all_3001_4000=readRDS(file="T18_6_gfblup_prediction_all_3001_4000.rds")
+T18_6_gfblup_prediction_all_4001_5000=readRDS(file="T18_6_gfblup_prediction_all_4001_5000.rds")
+T18_6_gfblup_prediction_all_5001_6000=readRDS(file="T18_6_gfblup_prediction_all_5001_6000.rds")
+T18_6_gfblup_prediction_all_6001_7297=readRDS(file="T18_6_gfblup_prediction_all_6001_7297.rds")
+
+T18_6_gfblup_variances_all_1_1000=readRDS(file="T18_6_gfblup_variances_all_1_1000.rds")
+T18_6_gfblup_variances_all_1001_2000=readRDS(file="T18_6_gfblup_variances_all_1001_2000.rds")
+T18_6_gfblup_variances_all_2001_3000=readRDS(file="T18_6_gfblup_variances_all_2001_3000.rds")
+T18_6_gfblup_variances_all_3001_4000=readRDS(file="T18_6_gfblup_variances_all_3001_4000.rds")
+T18_6_gfblup_variances_all_4001_5000=readRDS(file="T18_6_gfblup_variances_all_4001_5000.rds")
+T18_6_gfblup_variances_all_5001_6000=readRDS(file="T18_6_gfblup_variances_all_5001_6000.rds")
+T18_6_gfblup_variances_all_6001_7297=readRDS(file="T18_6_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T18_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_6_gfblup_variances_all=rep(list(list()),cycles)
+T18_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_1_1000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_1001_2000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_2001_3000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_3001_4000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_4001_5000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_5001_6000[[r]])
+	T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_6001_7297[[r]])
+
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_1_1000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_1001_2000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_2001_3000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_3001_4000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_4001_5000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_5001_6000[[r]])
+	T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T18_6_gfblup_prediction_all,"T18_6_gfblup_prediction_all.rds")
+saveRDS(T18_6_gfblup_variances_all,"T18_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_7_gblup_prediction_all_1_1000=readRDS(file="T18_7_gblup_prediction_all_1_1000.rds")
+T18_7_gblup_prediction_all_1001_2000=readRDS(file="T18_7_gblup_prediction_all_1001_2000.rds")
+T18_7_gblup_prediction_all_2001_3000=readRDS(file="T18_7_gblup_prediction_all_2001_3000.rds")
+T18_7_gblup_prediction_all_3001_4000=readRDS(file="T18_7_gblup_prediction_all_3001_4000.rds")
+T18_7_gblup_prediction_all_4001_5000=readRDS(file="T18_7_gblup_prediction_all_4001_5000.rds")
+T18_7_gblup_prediction_all_5001_6000=readRDS(file="T18_7_gblup_prediction_all_5001_6000.rds")
+T18_7_gblup_prediction_all_6001_7297=readRDS(file="T18_7_gblup_prediction_all_6001_7297.rds")
+T18_7_gblup_prediction_all=c(T18_7_gblup_prediction_all_1_1000,T18_7_gblup_prediction_all_1001_2000,T18_7_gblup_prediction_all_2001_3000,T18_7_gblup_prediction_all_3001_4000,T18_7_gblup_prediction_all_4001_5000,T18_7_gblup_prediction_all_5001_6000,T18_7_gblup_prediction_all_6001_7297)
+
+T18_7_gblup_variances_all_1_1000=readRDS(file="T18_7_gblup_variances_all_1_1000.rds")
+T18_7_gblup_variances_all_1001_2000=readRDS(file="T18_7_gblup_variances_all_1001_2000.rds")
+T18_7_gblup_variances_all_2001_3000=readRDS(file="T18_7_gblup_variances_all_2001_3000.rds")
+T18_7_gblup_variances_all_3001_4000=readRDS(file="T18_7_gblup_variances_all_3001_4000.rds")
+T18_7_gblup_variances_all_4001_5000=readRDS(file="T18_7_gblup_variances_all_4001_5000.rds")
+T18_7_gblup_variances_all_5001_6000=readRDS(file="T18_7_gblup_variances_all_5001_6000.rds")
+T18_7_gblup_variances_all_6001_7297=readRDS(file="T18_7_gblup_variances_all_6001_7297.rds")
+T18_7_gblup_variances_all=c(T18_7_gblup_variances_all_1_1000,T18_7_gblup_variances_all_1001_2000,T18_7_gblup_variances_all_2001_3000,T18_7_gblup_variances_all_3001_4000,T18_7_gblup_variances_all_4001_5000,T18_7_gblup_variances_all_5001_6000,T18_7_gblup_variances_all_6001_7297)
+
+saveRDS(T18_7_gblup_prediction_all,"T18_7_gblup_prediction_all.rds")
+saveRDS(T18_7_gblup_variances_all,"T18_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_7_gfblup_prediction_all_1_1000=readRDS(file="T18_7_gfblup_prediction_all_1_1000.rds")
+T18_7_gfblup_prediction_all_1001_2000=readRDS(file="T18_7_gfblup_prediction_all_1001_2000.rds")
+T18_7_gfblup_prediction_all_2001_3000=readRDS(file="T18_7_gfblup_prediction_all_2001_3000.rds")
+T18_7_gfblup_prediction_all_3001_4000=readRDS(file="T18_7_gfblup_prediction_all_3001_4000.rds")
+T18_7_gfblup_prediction_all_4001_5000=readRDS(file="T18_7_gfblup_prediction_all_4001_5000.rds")
+T18_7_gfblup_prediction_all_5001_6000=readRDS(file="T18_7_gfblup_prediction_all_5001_6000.rds")
+T18_7_gfblup_prediction_all_6001_7297=readRDS(file="T18_7_gfblup_prediction_all_6001_7297.rds")
+
+T18_7_gfblup_variances_all_1_1000=readRDS(file="T18_7_gfblup_variances_all_1_1000.rds")
+T18_7_gfblup_variances_all_1001_2000=readRDS(file="T18_7_gfblup_variances_all_1001_2000.rds")
+T18_7_gfblup_variances_all_2001_3000=readRDS(file="T18_7_gfblup_variances_all_2001_3000.rds")
+T18_7_gfblup_variances_all_3001_4000=readRDS(file="T18_7_gfblup_variances_all_3001_4000.rds")
+T18_7_gfblup_variances_all_4001_5000=readRDS(file="T18_7_gfblup_variances_all_4001_5000.rds")
+T18_7_gfblup_variances_all_5001_6000=readRDS(file="T18_7_gfblup_variances_all_5001_6000.rds")
+T18_7_gfblup_variances_all_6001_7297=readRDS(file="T18_7_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T18_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_7_gfblup_variances_all=rep(list(list()),cycles)
+T18_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_1_1000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_1001_2000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_2001_3000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_3001_4000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_4001_5000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_5001_6000[[r]])
+	T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_6001_7297[[r]])
+
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_1_1000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_1001_2000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_2001_3000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_3001_4000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_4001_5000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_5001_6000[[r]])
+	T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T18_7_gfblup_prediction_all,"T18_7_gfblup_prediction_all.rds")
+saveRDS(T18_7_gfblup_variances_all,"T18_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_8_gblup_prediction_all_1_1000=readRDS(file="T18_8_gblup_prediction_all_1_1000.rds")
+T18_8_gblup_prediction_all_1001_2000=readRDS(file="T18_8_gblup_prediction_all_1001_2000.rds")
+T18_8_gblup_prediction_all_2001_3000=readRDS(file="T18_8_gblup_prediction_all_2001_3000.rds")
+T18_8_gblup_prediction_all_3001_4000=readRDS(file="T18_8_gblup_prediction_all_3001_4000.rds")
+T18_8_gblup_prediction_all_4001_5000=readRDS(file="T18_8_gblup_prediction_all_4001_5000.rds")
+T18_8_gblup_prediction_all_5001_6000=readRDS(file="T18_8_gblup_prediction_all_5001_6000.rds")
+T18_8_gblup_prediction_all_6001_7297=readRDS(file="T18_8_gblup_prediction_all_6001_7297.rds")
+T18_8_gblup_prediction_all=c(T18_8_gblup_prediction_all_1_1000,T18_8_gblup_prediction_all_1001_2000,T18_8_gblup_prediction_all_2001_3000,T18_8_gblup_prediction_all_3001_4000,T18_8_gblup_prediction_all_4001_5000,T18_8_gblup_prediction_all_5001_6000,T18_8_gblup_prediction_all_6001_7297)
+
+T18_8_gblup_variances_all_1_1000=readRDS(file="T18_8_gblup_variances_all_1_1000.rds")
+T18_8_gblup_variances_all_1001_2000=readRDS(file="T18_8_gblup_variances_all_1001_2000.rds")
+T18_8_gblup_variances_all_2001_3000=readRDS(file="T18_8_gblup_variances_all_2001_3000.rds")
+T18_8_gblup_variances_all_3001_4000=readRDS(file="T18_8_gblup_variances_all_3001_4000.rds")
+T18_8_gblup_variances_all_4001_5000=readRDS(file="T18_8_gblup_variances_all_4001_5000.rds")
+T18_8_gblup_variances_all_5001_6000=readRDS(file="T18_8_gblup_variances_all_5001_6000.rds")
+T18_8_gblup_variances_all_6001_7297=readRDS(file="T18_8_gblup_variances_all_6001_7297.rds")
+T18_8_gblup_variances_all=c(T18_8_gblup_variances_all_1_1000,T18_8_gblup_variances_all_1001_2000,T18_8_gblup_variances_all_2001_3000,T18_8_gblup_variances_all_3001_4000,T18_8_gblup_variances_all_4001_5000,T18_8_gblup_variances_all_5001_6000,T18_8_gblup_variances_all_6001_7297)
+
+saveRDS(T18_8_gblup_prediction_all,"T18_8_gblup_prediction_all.rds")
+saveRDS(T18_8_gblup_variances_all,"T18_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T18_8_gfblup_prediction_all_1_1000=readRDS(file="T18_8_gfblup_prediction_all_1_1000.rds")
+T18_8_gfblup_prediction_all_1001_2000=readRDS(file="T18_8_gfblup_prediction_all_1001_2000.rds")
+T18_8_gfblup_prediction_all_2001_3000=readRDS(file="T18_8_gfblup_prediction_all_2001_3000.rds")
+T18_8_gfblup_prediction_all_3001_4000=readRDS(file="T18_8_gfblup_prediction_all_3001_4000.rds")
+T18_8_gfblup_prediction_all_4001_5000=readRDS(file="T18_8_gfblup_prediction_all_4001_5000.rds")
+T18_8_gfblup_prediction_all_5001_6000=readRDS(file="T18_8_gfblup_prediction_all_5001_6000.rds")
+T18_8_gfblup_prediction_all_6001_7297=readRDS(file="T18_8_gfblup_prediction_all_6001_7297.rds")
+
+T18_8_gfblup_variances_all_1_1000=readRDS(file="T18_8_gfblup_variances_all_1_1000.rds")
+T18_8_gfblup_variances_all_1001_2000=readRDS(file="T18_8_gfblup_variances_all_1001_2000.rds")
+T18_8_gfblup_variances_all_2001_3000=readRDS(file="T18_8_gfblup_variances_all_2001_3000.rds")
+T18_8_gfblup_variances_all_3001_4000=readRDS(file="T18_8_gfblup_variances_all_3001_4000.rds")
+T18_8_gfblup_variances_all_4001_5000=readRDS(file="T18_8_gfblup_variances_all_4001_5000.rds")
+T18_8_gfblup_variances_all_5001_6000=readRDS(file="T18_8_gfblup_variances_all_5001_6000.rds")
+T18_8_gfblup_variances_all_6001_7297=readRDS(file="T18_8_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T18_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T18_8_gfblup_variances_all=rep(list(list()),cycles)
+T18_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_1_1000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_1001_2000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_2001_3000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_3001_4000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_4001_5000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_5001_6000[[r]])
+	T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_6001_7297[[r]])
+
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_1_1000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_1001_2000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_2001_3000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_3001_4000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_4001_5000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_5001_6000[[r]])
+	T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T18_8_gfblup_prediction_all,"T18_8_gfblup_prediction_all.rds")
+saveRDS(T18_8_gfblup_variances_all,"T18_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_1_gblup_prediction_all_1_1000=readRDS(file="T19_1_gblup_prediction_all_1_1000.rds")
+T19_1_gblup_prediction_all_1001_2000=readRDS(file="T19_1_gblup_prediction_all_1001_2000.rds")
+T19_1_gblup_prediction_all_2001_3000=readRDS(file="T19_1_gblup_prediction_all_2001_3000.rds")
+T19_1_gblup_prediction_all_3001_4000=readRDS(file="T19_1_gblup_prediction_all_3001_4000.rds")
+T19_1_gblup_prediction_all_4001_5000=readRDS(file="T19_1_gblup_prediction_all_4001_5000.rds")
+T19_1_gblup_prediction_all_5001_6000=readRDS(file="T19_1_gblup_prediction_all_5001_6000.rds")
+T19_1_gblup_prediction_all_6001_7297=readRDS(file="T19_1_gblup_prediction_all_6001_7297.rds")
+T19_1_gblup_prediction_all=c(T19_1_gblup_prediction_all_1_1000,T19_1_gblup_prediction_all_1001_2000,T19_1_gblup_prediction_all_2001_3000,T19_1_gblup_prediction_all_3001_4000,T19_1_gblup_prediction_all_4001_5000,T19_1_gblup_prediction_all_5001_6000,T19_1_gblup_prediction_all_6001_7297)
+
+T19_1_gblup_variances_all_1_1000=readRDS(file="T19_1_gblup_variances_all_1_1000.rds")
+T19_1_gblup_variances_all_1001_2000=readRDS(file="T19_1_gblup_variances_all_1001_2000.rds")
+T19_1_gblup_variances_all_2001_3000=readRDS(file="T19_1_gblup_variances_all_2001_3000.rds")
+T19_1_gblup_variances_all_3001_4000=readRDS(file="T19_1_gblup_variances_all_3001_4000.rds")
+T19_1_gblup_variances_all_4001_5000=readRDS(file="T19_1_gblup_variances_all_4001_5000.rds")
+T19_1_gblup_variances_all_5001_6000=readRDS(file="T19_1_gblup_variances_all_5001_6000.rds")
+T19_1_gblup_variances_all_6001_7297=readRDS(file="T19_1_gblup_variances_all_6001_7297.rds")
+T19_1_gblup_variances_all=c(T19_1_gblup_variances_all_1_1000,T19_1_gblup_variances_all_1001_2000,T19_1_gblup_variances_all_2001_3000,T19_1_gblup_variances_all_3001_4000,T19_1_gblup_variances_all_4001_5000,T19_1_gblup_variances_all_5001_6000,T19_1_gblup_variances_all_6001_7297)
+
+saveRDS(T19_1_gblup_prediction_all,"T19_1_gblup_prediction_all.rds")
+saveRDS(T19_1_gblup_variances_all,"T19_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_1_gfblup_prediction_all_1_1000=readRDS(file="T19_1_gfblup_prediction_all_1_1000.rds")
+T19_1_gfblup_prediction_all_1001_2000=readRDS(file="T19_1_gfblup_prediction_all_1001_2000.rds")
+T19_1_gfblup_prediction_all_2001_3000=readRDS(file="T19_1_gfblup_prediction_all_2001_3000.rds")
+T19_1_gfblup_prediction_all_3001_4000=readRDS(file="T19_1_gfblup_prediction_all_3001_4000.rds")
+T19_1_gfblup_prediction_all_4001_5000=readRDS(file="T19_1_gfblup_prediction_all_4001_5000.rds")
+T19_1_gfblup_prediction_all_5001_6000=readRDS(file="T19_1_gfblup_prediction_all_5001_6000.rds")
+T19_1_gfblup_prediction_all_6001_7297=readRDS(file="T19_1_gfblup_prediction_all_6001_7297.rds")
+
+T19_1_gfblup_variances_all_1_1000=readRDS(file="T19_1_gfblup_variances_all_1_1000.rds")
+T19_1_gfblup_variances_all_1001_2000=readRDS(file="T19_1_gfblup_variances_all_1001_2000.rds")
+T19_1_gfblup_variances_all_2001_3000=readRDS(file="T19_1_gfblup_variances_all_2001_3000.rds")
+T19_1_gfblup_variances_all_3001_4000=readRDS(file="T19_1_gfblup_variances_all_3001_4000.rds")
+T19_1_gfblup_variances_all_4001_5000=readRDS(file="T19_1_gfblup_variances_all_4001_5000.rds")
+T19_1_gfblup_variances_all_5001_6000=readRDS(file="T19_1_gfblup_variances_all_5001_6000.rds")
+T19_1_gfblup_variances_all_6001_7297=readRDS(file="T19_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T19_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_1_gfblup_variances_all=rep(list(list()),cycles)
+T19_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_1_1000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_1001_2000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_2001_3000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_3001_4000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_4001_5000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_5001_6000[[r]])
+	T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_6001_7297[[r]])
+
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_1_1000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_1001_2000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_2001_3000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_3001_4000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_4001_5000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_5001_6000[[r]])
+	T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T19_1_gfblup_prediction_all,"T19_1_gfblup_prediction_all.rds")
+saveRDS(T19_1_gfblup_variances_all,"T19_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_2_gblup_prediction_all_1_1000=readRDS(file="T19_2_gblup_prediction_all_1_1000.rds")
+T19_2_gblup_prediction_all_1001_2000=readRDS(file="T19_2_gblup_prediction_all_1001_2000.rds")
+T19_2_gblup_prediction_all_2001_3000=readRDS(file="T19_2_gblup_prediction_all_2001_3000.rds")
+T19_2_gblup_prediction_all_3001_4000=readRDS(file="T19_2_gblup_prediction_all_3001_4000.rds")
+T19_2_gblup_prediction_all_4001_5000=readRDS(file="T19_2_gblup_prediction_all_4001_5000.rds")
+T19_2_gblup_prediction_all_5001_6000=readRDS(file="T19_2_gblup_prediction_all_5001_6000.rds")
+T19_2_gblup_prediction_all_6001_7297=readRDS(file="T19_2_gblup_prediction_all_6001_7297.rds")
+T19_2_gblup_prediction_all=c(T19_2_gblup_prediction_all_1_1000,T19_2_gblup_prediction_all_1001_2000,T19_2_gblup_prediction_all_2001_3000,T19_2_gblup_prediction_all_3001_4000,T19_2_gblup_prediction_all_4001_5000,T19_2_gblup_prediction_all_5001_6000,T19_2_gblup_prediction_all_6001_7297)
+
+T19_2_gblup_variances_all_1_1000=readRDS(file="T19_2_gblup_variances_all_1_1000.rds")
+T19_2_gblup_variances_all_1001_2000=readRDS(file="T19_2_gblup_variances_all_1001_2000.rds")
+T19_2_gblup_variances_all_2001_3000=readRDS(file="T19_2_gblup_variances_all_2001_3000.rds")
+T19_2_gblup_variances_all_3001_4000=readRDS(file="T19_2_gblup_variances_all_3001_4000.rds")
+T19_2_gblup_variances_all_4001_5000=readRDS(file="T19_2_gblup_variances_all_4001_5000.rds")
+T19_2_gblup_variances_all_5001_6000=readRDS(file="T19_2_gblup_variances_all_5001_6000.rds")
+T19_2_gblup_variances_all_6001_7297=readRDS(file="T19_2_gblup_variances_all_6001_7297.rds")
+T19_2_gblup_variances_all=c(T19_2_gblup_variances_all_1_1000,T19_2_gblup_variances_all_1001_2000,T19_2_gblup_variances_all_2001_3000,T19_2_gblup_variances_all_3001_4000,T19_2_gblup_variances_all_4001_5000,T19_2_gblup_variances_all_5001_6000,T19_2_gblup_variances_all_6001_7297)
+
+saveRDS(T19_2_gblup_prediction_all,"T19_2_gblup_prediction_all.rds")
+saveRDS(T19_2_gblup_variances_all,"T19_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_2_gfblup_prediction_all_1_1000=readRDS(file="T19_2_gfblup_prediction_all_1_1000.rds")
+T19_2_gfblup_prediction_all_1001_2000=readRDS(file="T19_2_gfblup_prediction_all_1001_2000.rds")
+T19_2_gfblup_prediction_all_2001_3000=readRDS(file="T19_2_gfblup_prediction_all_2001_3000.rds")
+T19_2_gfblup_prediction_all_3001_4000=readRDS(file="T19_2_gfblup_prediction_all_3001_4000.rds")
+T19_2_gfblup_prediction_all_4001_5000=readRDS(file="T19_2_gfblup_prediction_all_4001_5000.rds")
+T19_2_gfblup_prediction_all_5001_6000=readRDS(file="T19_2_gfblup_prediction_all_5001_6000.rds")
+T19_2_gfblup_prediction_all_6001_7297=readRDS(file="T19_2_gfblup_prediction_all_6001_7297.rds")
+
+T19_2_gfblup_variances_all_1_1000=readRDS(file="T19_2_gfblup_variances_all_1_1000.rds")
+T19_2_gfblup_variances_all_1001_2000=readRDS(file="T19_2_gfblup_variances_all_1001_2000.rds")
+T19_2_gfblup_variances_all_2001_3000=readRDS(file="T19_2_gfblup_variances_all_2001_3000.rds")
+T19_2_gfblup_variances_all_3001_4000=readRDS(file="T19_2_gfblup_variances_all_3001_4000.rds")
+T19_2_gfblup_variances_all_4001_5000=readRDS(file="T19_2_gfblup_variances_all_4001_5000.rds")
+T19_2_gfblup_variances_all_5001_6000=readRDS(file="T19_2_gfblup_variances_all_5001_6000.rds")
+T19_2_gfblup_variances_all_6001_7297=readRDS(file="T19_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T19_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_2_gfblup_variances_all=rep(list(list()),cycles)
+T19_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_1_1000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_1001_2000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_2001_3000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_3001_4000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_4001_5000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_5001_6000[[r]])
+	T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_6001_7297[[r]])
+
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_1_1000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_1001_2000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_2001_3000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_3001_4000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_4001_5000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_5001_6000[[r]])
+	T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T19_2_gfblup_prediction_all,"T19_2_gfblup_prediction_all.rds")
+saveRDS(T19_2_gfblup_variances_all,"T19_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_3_gblup_prediction_all_1_1000=readRDS(file="T19_3_gblup_prediction_all_1_1000.rds")
+T19_3_gblup_prediction_all_1001_2000=readRDS(file="T19_3_gblup_prediction_all_1001_2000.rds")
+T19_3_gblup_prediction_all_2001_3000=readRDS(file="T19_3_gblup_prediction_all_2001_3000.rds")
+T19_3_gblup_prediction_all_3001_4000=readRDS(file="T19_3_gblup_prediction_all_3001_4000.rds")
+T19_3_gblup_prediction_all_4001_5000=readRDS(file="T19_3_gblup_prediction_all_4001_5000.rds")
+T19_3_gblup_prediction_all_5001_6000=readRDS(file="T19_3_gblup_prediction_all_5001_6000.rds")
+T19_3_gblup_prediction_all_6001_7297=readRDS(file="T19_3_gblup_prediction_all_6001_7297.rds")
+T19_3_gblup_prediction_all=c(T19_3_gblup_prediction_all_1_1000,T19_3_gblup_prediction_all_1001_2000,T19_3_gblup_prediction_all_2001_3000,T19_3_gblup_prediction_all_3001_4000,T19_3_gblup_prediction_all_4001_5000,T19_3_gblup_prediction_all_5001_6000,T19_3_gblup_prediction_all_6001_7297)
+
+T19_3_gblup_variances_all_1_1000=readRDS(file="T19_3_gblup_variances_all_1_1000.rds")
+T19_3_gblup_variances_all_1001_2000=readRDS(file="T19_3_gblup_variances_all_1001_2000.rds")
+T19_3_gblup_variances_all_2001_3000=readRDS(file="T19_3_gblup_variances_all_2001_3000.rds")
+T19_3_gblup_variances_all_3001_4000=readRDS(file="T19_3_gblup_variances_all_3001_4000.rds")
+T19_3_gblup_variances_all_4001_5000=readRDS(file="T19_3_gblup_variances_all_4001_5000.rds")
+T19_3_gblup_variances_all_5001_6000=readRDS(file="T19_3_gblup_variances_all_5001_6000.rds")
+T19_3_gblup_variances_all_6001_7297=readRDS(file="T19_3_gblup_variances_all_6001_7297.rds")
+T19_3_gblup_variances_all=c(T19_3_gblup_variances_all_1_1000,T19_3_gblup_variances_all_1001_2000,T19_3_gblup_variances_all_2001_3000,T19_3_gblup_variances_all_3001_4000,T19_3_gblup_variances_all_4001_5000,T19_3_gblup_variances_all_5001_6000,T19_3_gblup_variances_all_6001_7297)
+
+saveRDS(T19_3_gblup_prediction_all,"T19_3_gblup_prediction_all.rds")
+saveRDS(T19_3_gblup_variances_all,"T19_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_3_gfblup_prediction_all_1_1000=readRDS(file="T19_3_gfblup_prediction_all_1_1000.rds")
+T19_3_gfblup_prediction_all_1001_2000=readRDS(file="T19_3_gfblup_prediction_all_1001_2000.rds")
+T19_3_gfblup_prediction_all_2001_3000=readRDS(file="T19_3_gfblup_prediction_all_2001_3000.rds")
+T19_3_gfblup_prediction_all_3001_4000=readRDS(file="T19_3_gfblup_prediction_all_3001_4000.rds")
+T19_3_gfblup_prediction_all_4001_5000=readRDS(file="T19_3_gfblup_prediction_all_4001_5000.rds")
+T19_3_gfblup_prediction_all_5001_6000=readRDS(file="T19_3_gfblup_prediction_all_5001_6000.rds")
+T19_3_gfblup_prediction_all_6001_7297=readRDS(file="T19_3_gfblup_prediction_all_6001_7297.rds")
+
+T19_3_gfblup_variances_all_1_1000=readRDS(file="T19_3_gfblup_variances_all_1_1000.rds")
+T19_3_gfblup_variances_all_1001_2000=readRDS(file="T19_3_gfblup_variances_all_1001_2000.rds")
+T19_3_gfblup_variances_all_2001_3000=readRDS(file="T19_3_gfblup_variances_all_2001_3000.rds")
+T19_3_gfblup_variances_all_3001_4000=readRDS(file="T19_3_gfblup_variances_all_3001_4000.rds")
+T19_3_gfblup_variances_all_4001_5000=readRDS(file="T19_3_gfblup_variances_all_4001_5000.rds")
+T19_3_gfblup_variances_all_5001_6000=readRDS(file="T19_3_gfblup_variances_all_5001_6000.rds")
+T19_3_gfblup_variances_all_6001_7297=readRDS(file="T19_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T19_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_3_gfblup_variances_all=rep(list(list()),cycles)
+T19_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_1_1000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_1001_2000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_2001_3000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_3001_4000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_4001_5000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_5001_6000[[r]])
+	T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_6001_7297[[r]])
+
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_1_1000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_1001_2000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_2001_3000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_3001_4000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_4001_5000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_5001_6000[[r]])
+	T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T19_3_gfblup_prediction_all,"T19_3_gfblup_prediction_all.rds")
+saveRDS(T19_3_gfblup_variances_all,"T19_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_4_gblup_prediction_all_1_1000=readRDS(file="T19_4_gblup_prediction_all_1_1000.rds")
+T19_4_gblup_prediction_all_1001_2000=readRDS(file="T19_4_gblup_prediction_all_1001_2000.rds")
+T19_4_gblup_prediction_all_2001_3000=readRDS(file="T19_4_gblup_prediction_all_2001_3000.rds")
+T19_4_gblup_prediction_all_3001_4000=readRDS(file="T19_4_gblup_prediction_all_3001_4000.rds")
+T19_4_gblup_prediction_all_4001_5000=readRDS(file="T19_4_gblup_prediction_all_4001_5000.rds")
+T19_4_gblup_prediction_all_5001_6000=readRDS(file="T19_4_gblup_prediction_all_5001_6000.rds")
+T19_4_gblup_prediction_all_6001_7297=readRDS(file="T19_4_gblup_prediction_all_6001_7297.rds")
+T19_4_gblup_prediction_all=c(T19_4_gblup_prediction_all_1_1000,T19_4_gblup_prediction_all_1001_2000,T19_4_gblup_prediction_all_2001_3000,T19_4_gblup_prediction_all_3001_4000,T19_4_gblup_prediction_all_4001_5000,T19_4_gblup_prediction_all_5001_6000,T19_4_gblup_prediction_all_6001_7297)
+
+T19_4_gblup_variances_all_1_1000=readRDS(file="T19_4_gblup_variances_all_1_1000.rds")
+T19_4_gblup_variances_all_1001_2000=readRDS(file="T19_4_gblup_variances_all_1001_2000.rds")
+T19_4_gblup_variances_all_2001_3000=readRDS(file="T19_4_gblup_variances_all_2001_3000.rds")
+T19_4_gblup_variances_all_3001_4000=readRDS(file="T19_4_gblup_variances_all_3001_4000.rds")
+T19_4_gblup_variances_all_4001_5000=readRDS(file="T19_4_gblup_variances_all_4001_5000.rds")
+T19_4_gblup_variances_all_5001_6000=readRDS(file="T19_4_gblup_variances_all_5001_6000.rds")
+T19_4_gblup_variances_all_6001_7297=readRDS(file="T19_4_gblup_variances_all_6001_7297.rds")
+T19_4_gblup_variances_all=c(T19_4_gblup_variances_all_1_1000,T19_4_gblup_variances_all_1001_2000,T19_4_gblup_variances_all_2001_3000,T19_4_gblup_variances_all_3001_4000,T19_4_gblup_variances_all_4001_5000,T19_4_gblup_variances_all_5001_6000,T19_4_gblup_variances_all_6001_7297)
+
+saveRDS(T19_4_gblup_prediction_all,"T19_4_gblup_prediction_all.rds")
+saveRDS(T19_4_gblup_variances_all,"T19_4_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_4_gfblup_prediction_all_1_1000=readRDS(file="T19_4_gfblup_prediction_all_1_1000.rds")
+T19_4_gfblup_prediction_all_1001_2000=readRDS(file="T19_4_gfblup_prediction_all_1001_2000.rds")
+T19_4_gfblup_prediction_all_2001_3000=readRDS(file="T19_4_gfblup_prediction_all_2001_3000.rds")
+T19_4_gfblup_prediction_all_3001_4000=readRDS(file="T19_4_gfblup_prediction_all_3001_4000.rds")
+T19_4_gfblup_prediction_all_4001_5000=readRDS(file="T19_4_gfblup_prediction_all_4001_5000.rds")
+T19_4_gfblup_prediction_all_5001_6000=readRDS(file="T19_4_gfblup_prediction_all_5001_6000.rds")
+T19_4_gfblup_prediction_all_6001_7297=readRDS(file="T19_4_gfblup_prediction_all_6001_7297.rds")
+
+T19_4_gfblup_variances_all_1_1000=readRDS(file="T19_4_gfblup_variances_all_1_1000.rds")
+T19_4_gfblup_variances_all_1001_2000=readRDS(file="T19_4_gfblup_variances_all_1001_2000.rds")
+T19_4_gfblup_variances_all_2001_3000=readRDS(file="T19_4_gfblup_variances_all_2001_3000.rds")
+T19_4_gfblup_variances_all_3001_4000=readRDS(file="T19_4_gfblup_variances_all_3001_4000.rds")
+T19_4_gfblup_variances_all_4001_5000=readRDS(file="T19_4_gfblup_variances_all_4001_5000.rds")
+T19_4_gfblup_variances_all_5001_6000=readRDS(file="T19_4_gfblup_variances_all_5001_6000.rds")
+T19_4_gfblup_variances_all_6001_7297=readRDS(file="T19_4_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T19_4_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_4_gfblup_variances_all=rep(list(list()),cycles)
+T19_4_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_1_1000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_1001_2000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_2001_3000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_3001_4000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_4001_5000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_5001_6000[[r]])
+	T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_6001_7297[[r]])
+
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_1_1000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_1001_2000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_2001_3000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_3001_4000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_4001_5000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_5001_6000[[r]])
+	T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T19_4_gfblup_prediction_all,"T19_4_gfblup_prediction_all.rds")
+saveRDS(T19_4_gfblup_variances_all,"T19_4_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_5_gblup_prediction_all_1_1000=readRDS(file="T19_5_gblup_prediction_all_1_1000.rds")
+T19_5_gblup_prediction_all_1001_2000=readRDS(file="T19_5_gblup_prediction_all_1001_2000.rds")
+T19_5_gblup_prediction_all_2001_3000=readRDS(file="T19_5_gblup_prediction_all_2001_3000.rds")
+T19_5_gblup_prediction_all_3001_4000=readRDS(file="T19_5_gblup_prediction_all_3001_4000.rds")
+T19_5_gblup_prediction_all_4001_5000=readRDS(file="T19_5_gblup_prediction_all_4001_5000.rds")
+T19_5_gblup_prediction_all_5001_6000=readRDS(file="T19_5_gblup_prediction_all_5001_6000.rds")
+T19_5_gblup_prediction_all_6001_7297=readRDS(file="T19_5_gblup_prediction_all_6001_7297.rds")
+T19_5_gblup_prediction_all=c(T19_5_gblup_prediction_all_1_1000,T19_5_gblup_prediction_all_1001_2000,T19_5_gblup_prediction_all_2001_3000,T19_5_gblup_prediction_all_3001_4000,T19_5_gblup_prediction_all_4001_5000,T19_5_gblup_prediction_all_5001_6000,T19_5_gblup_prediction_all_6001_7297)
+
+T19_5_gblup_variances_all_1_1000=readRDS(file="T19_5_gblup_variances_all_1_1000.rds")
+T19_5_gblup_variances_all_1001_2000=readRDS(file="T19_5_gblup_variances_all_1001_2000.rds")
+T19_5_gblup_variances_all_2001_3000=readRDS(file="T19_5_gblup_variances_all_2001_3000.rds")
+T19_5_gblup_variances_all_3001_4000=readRDS(file="T19_5_gblup_variances_all_3001_4000.rds")
+T19_5_gblup_variances_all_4001_5000=readRDS(file="T19_5_gblup_variances_all_4001_5000.rds")
+T19_5_gblup_variances_all_5001_6000=readRDS(file="T19_5_gblup_variances_all_5001_6000.rds")
+T19_5_gblup_variances_all_6001_7297=readRDS(file="T19_5_gblup_variances_all_6001_7297.rds")
+T19_5_gblup_variances_all=c(T19_5_gblup_variances_all_1_1000,T19_5_gblup_variances_all_1001_2000,T19_5_gblup_variances_all_2001_3000,T19_5_gblup_variances_all_3001_4000,T19_5_gblup_variances_all_4001_5000,T19_5_gblup_variances_all_5001_6000,T19_5_gblup_variances_all_6001_7297)
+
+saveRDS(T19_5_gblup_prediction_all,"T19_5_gblup_prediction_all.rds")
+saveRDS(T19_5_gblup_variances_all,"T19_5_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_5_gfblup_prediction_all_1_1000=readRDS(file="T19_5_gfblup_prediction_all_1_1000.rds")
+T19_5_gfblup_prediction_all_1001_2000=readRDS(file="T19_5_gfblup_prediction_all_1001_2000.rds")
+T19_5_gfblup_prediction_all_2001_3000=readRDS(file="T19_5_gfblup_prediction_all_2001_3000.rds")
+T19_5_gfblup_prediction_all_3001_4000=readRDS(file="T19_5_gfblup_prediction_all_3001_4000.rds")
+T19_5_gfblup_prediction_all_4001_5000=readRDS(file="T19_5_gfblup_prediction_all_4001_5000.rds")
+T19_5_gfblup_prediction_all_5001_6000=readRDS(file="T19_5_gfblup_prediction_all_5001_6000.rds")
+T19_5_gfblup_prediction_all_6001_7297=readRDS(file="T19_5_gfblup_prediction_all_6001_7297.rds")
+
+T19_5_gfblup_variances_all_1_1000=readRDS(file="T19_5_gfblup_variances_all_1_1000.rds")
+T19_5_gfblup_variances_all_1001_2000=readRDS(file="T19_5_gfblup_variances_all_1001_2000.rds")
+T19_5_gfblup_variances_all_2001_3000=readRDS(file="T19_5_gfblup_variances_all_2001_3000.rds")
+T19_5_gfblup_variances_all_3001_4000=readRDS(file="T19_5_gfblup_variances_all_3001_4000.rds")
+T19_5_gfblup_variances_all_4001_5000=readRDS(file="T19_5_gfblup_variances_all_4001_5000.rds")
+T19_5_gfblup_variances_all_5001_6000=readRDS(file="T19_5_gfblup_variances_all_5001_6000.rds")
+T19_5_gfblup_variances_all_6001_7297=readRDS(file="T19_5_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T19_5_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_5_gfblup_variances_all=rep(list(list()),cycles)
+T19_5_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_1_1000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_1001_2000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_2001_3000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_3001_4000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_4001_5000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_5001_6000[[r]])
+	T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_6001_7297[[r]])
+
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_1_1000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_1001_2000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_2001_3000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_3001_4000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_4001_5000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_5001_6000[[r]])
+	T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T19_5_gfblup_prediction_all,"T19_5_gfblup_prediction_all.rds")
+saveRDS(T19_5_gfblup_variances_all,"T19_5_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_6_gblup_prediction_all_1_1000=readRDS(file="T19_6_gblup_prediction_all_1_1000.rds")
+T19_6_gblup_prediction_all_1001_2000=readRDS(file="T19_6_gblup_prediction_all_1001_2000.rds")
+T19_6_gblup_prediction_all_2001_3000=readRDS(file="T19_6_gblup_prediction_all_2001_3000.rds")
+T19_6_gblup_prediction_all_3001_4000=readRDS(file="T19_6_gblup_prediction_all_3001_4000.rds")
+T19_6_gblup_prediction_all_4001_5000=readRDS(file="T19_6_gblup_prediction_all_4001_5000.rds")
+T19_6_gblup_prediction_all_5001_6000=readRDS(file="T19_6_gblup_prediction_all_5001_6000.rds")
+T19_6_gblup_prediction_all_6001_7297=readRDS(file="T19_6_gblup_prediction_all_6001_7297.rds")
+T19_6_gblup_prediction_all=c(T19_6_gblup_prediction_all_1_1000,T19_6_gblup_prediction_all_1001_2000,T19_6_gblup_prediction_all_2001_3000,T19_6_gblup_prediction_all_3001_4000,T19_6_gblup_prediction_all_4001_5000,T19_6_gblup_prediction_all_5001_6000,T19_6_gblup_prediction_all_6001_7297)
+
+T19_6_gblup_variances_all_1_1000=readRDS(file="T19_6_gblup_variances_all_1_1000.rds")
+T19_6_gblup_variances_all_1001_2000=readRDS(file="T19_6_gblup_variances_all_1001_2000.rds")
+T19_6_gblup_variances_all_2001_3000=readRDS(file="T19_6_gblup_variances_all_2001_3000.rds")
+T19_6_gblup_variances_all_3001_4000=readRDS(file="T19_6_gblup_variances_all_3001_4000.rds")
+T19_6_gblup_variances_all_4001_5000=readRDS(file="T19_6_gblup_variances_all_4001_5000.rds")
+T19_6_gblup_variances_all_5001_6000=readRDS(file="T19_6_gblup_variances_all_5001_6000.rds")
+T19_6_gblup_variances_all_6001_7297=readRDS(file="T19_6_gblup_variances_all_6001_7297.rds")
+T19_6_gblup_variances_all=c(T19_6_gblup_variances_all_1_1000,T19_6_gblup_variances_all_1001_2000,T19_6_gblup_variances_all_2001_3000,T19_6_gblup_variances_all_3001_4000,T19_6_gblup_variances_all_4001_5000,T19_6_gblup_variances_all_5001_6000,T19_6_gblup_variances_all_6001_7297)
+
+saveRDS(T19_6_gblup_prediction_all,"T19_6_gblup_prediction_all.rds")
+saveRDS(T19_6_gblup_variances_all,"T19_6_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_6_gfblup_prediction_all_1_1000=readRDS(file="T19_6_gfblup_prediction_all_1_1000.rds")
+T19_6_gfblup_prediction_all_1001_2000=readRDS(file="T19_6_gfblup_prediction_all_1001_2000.rds")
+T19_6_gfblup_prediction_all_2001_3000=readRDS(file="T19_6_gfblup_prediction_all_2001_3000.rds")
+T19_6_gfblup_prediction_all_3001_4000=readRDS(file="T19_6_gfblup_prediction_all_3001_4000.rds")
+T19_6_gfblup_prediction_all_4001_5000=readRDS(file="T19_6_gfblup_prediction_all_4001_5000.rds")
+T19_6_gfblup_prediction_all_5001_6000=readRDS(file="T19_6_gfblup_prediction_all_5001_6000.rds")
+T19_6_gfblup_prediction_all_6001_7297=readRDS(file="T19_6_gfblup_prediction_all_6001_7297.rds")
+
+T19_6_gfblup_variances_all_1_1000=readRDS(file="T19_6_gfblup_variances_all_1_1000.rds")
+T19_6_gfblup_variances_all_1001_2000=readRDS(file="T19_6_gfblup_variances_all_1001_2000.rds")
+T19_6_gfblup_variances_all_2001_3000=readRDS(file="T19_6_gfblup_variances_all_2001_3000.rds")
+T19_6_gfblup_variances_all_3001_4000=readRDS(file="T19_6_gfblup_variances_all_3001_4000.rds")
+T19_6_gfblup_variances_all_4001_5000=readRDS(file="T19_6_gfblup_variances_all_4001_5000.rds")
+T19_6_gfblup_variances_all_5001_6000=readRDS(file="T19_6_gfblup_variances_all_5001_6000.rds")
+T19_6_gfblup_variances_all_6001_7297=readRDS(file="T19_6_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T19_6_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_6_gfblup_variances_all=rep(list(list()),cycles)
+T19_6_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_1_1000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_1001_2000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_2001_3000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_3001_4000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_4001_5000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_5001_6000[[r]])
+	T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_6001_7297[[r]])
+
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_1_1000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_1001_2000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_2001_3000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_3001_4000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_4001_5000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_5001_6000[[r]])
+	T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T19_6_gfblup_prediction_all,"T19_6_gfblup_prediction_all.rds")
+saveRDS(T19_6_gfblup_variances_all,"T19_6_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_7_gblup_prediction_all_1_1000=readRDS(file="T19_7_gblup_prediction_all_1_1000.rds")
+T19_7_gblup_prediction_all_1001_2000=readRDS(file="T19_7_gblup_prediction_all_1001_2000.rds")
+T19_7_gblup_prediction_all_2001_3000=readRDS(file="T19_7_gblup_prediction_all_2001_3000.rds")
+T19_7_gblup_prediction_all_3001_4000=readRDS(file="T19_7_gblup_prediction_all_3001_4000.rds")
+T19_7_gblup_prediction_all_4001_5000=readRDS(file="T19_7_gblup_prediction_all_4001_5000.rds")
+T19_7_gblup_prediction_all_5001_6000=readRDS(file="T19_7_gblup_prediction_all_5001_6000.rds")
+T19_7_gblup_prediction_all_6001_7297=readRDS(file="T19_7_gblup_prediction_all_6001_7297.rds")
+T19_7_gblup_prediction_all=c(T19_7_gblup_prediction_all_1_1000,T19_7_gblup_prediction_all_1001_2000,T19_7_gblup_prediction_all_2001_3000,T19_7_gblup_prediction_all_3001_4000,T19_7_gblup_prediction_all_4001_5000,T19_7_gblup_prediction_all_5001_6000,T19_7_gblup_prediction_all_6001_7297)
+
+T19_7_gblup_variances_all_1_1000=readRDS(file="T19_7_gblup_variances_all_1_1000.rds")
+T19_7_gblup_variances_all_1001_2000=readRDS(file="T19_7_gblup_variances_all_1001_2000.rds")
+T19_7_gblup_variances_all_2001_3000=readRDS(file="T19_7_gblup_variances_all_2001_3000.rds")
+T19_7_gblup_variances_all_3001_4000=readRDS(file="T19_7_gblup_variances_all_3001_4000.rds")
+T19_7_gblup_variances_all_4001_5000=readRDS(file="T19_7_gblup_variances_all_4001_5000.rds")
+T19_7_gblup_variances_all_5001_6000=readRDS(file="T19_7_gblup_variances_all_5001_6000.rds")
+T19_7_gblup_variances_all_6001_7297=readRDS(file="T19_7_gblup_variances_all_6001_7297.rds")
+T19_7_gblup_variances_all=c(T19_7_gblup_variances_all_1_1000,T19_7_gblup_variances_all_1001_2000,T19_7_gblup_variances_all_2001_3000,T19_7_gblup_variances_all_3001_4000,T19_7_gblup_variances_all_4001_5000,T19_7_gblup_variances_all_5001_6000,T19_7_gblup_variances_all_6001_7297)
+
+saveRDS(T19_7_gblup_prediction_all,"T19_7_gblup_prediction_all.rds")
+saveRDS(T19_7_gblup_variances_all,"T19_7_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_7_gfblup_prediction_all_1_1000=readRDS(file="T19_7_gfblup_prediction_all_1_1000.rds")
+T19_7_gfblup_prediction_all_1001_2000=readRDS(file="T19_7_gfblup_prediction_all_1001_2000.rds")
+T19_7_gfblup_prediction_all_2001_3000=readRDS(file="T19_7_gfblup_prediction_all_2001_3000.rds")
+T19_7_gfblup_prediction_all_3001_4000=readRDS(file="T19_7_gfblup_prediction_all_3001_4000.rds")
+T19_7_gfblup_prediction_all_4001_5000=readRDS(file="T19_7_gfblup_prediction_all_4001_5000.rds")
+T19_7_gfblup_prediction_all_5001_6000=readRDS(file="T19_7_gfblup_prediction_all_5001_6000.rds")
+T19_7_gfblup_prediction_all_6001_7297=readRDS(file="T19_7_gfblup_prediction_all_6001_7297.rds")
+
+T19_7_gfblup_variances_all_1_1000=readRDS(file="T19_7_gfblup_variances_all_1_1000.rds")
+T19_7_gfblup_variances_all_1001_2000=readRDS(file="T19_7_gfblup_variances_all_1001_2000.rds")
+T19_7_gfblup_variances_all_2001_3000=readRDS(file="T19_7_gfblup_variances_all_2001_3000.rds")
+T19_7_gfblup_variances_all_3001_4000=readRDS(file="T19_7_gfblup_variances_all_3001_4000.rds")
+T19_7_gfblup_variances_all_4001_5000=readRDS(file="T19_7_gfblup_variances_all_4001_5000.rds")
+T19_7_gfblup_variances_all_5001_6000=readRDS(file="T19_7_gfblup_variances_all_5001_6000.rds")
+T19_7_gfblup_variances_all_6001_7297=readRDS(file="T19_7_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T19_7_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_7_gfblup_variances_all=rep(list(list()),cycles)
+T19_7_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_1_1000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_1001_2000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_2001_3000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_3001_4000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_4001_5000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_5001_6000[[r]])
+	T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_6001_7297[[r]])
+
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_1_1000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_1001_2000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_2001_3000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_3001_4000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_4001_5000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_5001_6000[[r]])
+	T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T19_7_gfblup_prediction_all,"T19_7_gfblup_prediction_all.rds")
+saveRDS(T19_7_gfblup_variances_all,"T19_7_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_8_gblup_prediction_all_1_1000=readRDS(file="T19_8_gblup_prediction_all_1_1000.rds")
+T19_8_gblup_prediction_all_1001_2000=readRDS(file="T19_8_gblup_prediction_all_1001_2000.rds")
+T19_8_gblup_prediction_all_2001_3000=readRDS(file="T19_8_gblup_prediction_all_2001_3000.rds")
+T19_8_gblup_prediction_all_3001_4000=readRDS(file="T19_8_gblup_prediction_all_3001_4000.rds")
+T19_8_gblup_prediction_all_4001_5000=readRDS(file="T19_8_gblup_prediction_all_4001_5000.rds")
+T19_8_gblup_prediction_all_5001_6000=readRDS(file="T19_8_gblup_prediction_all_5001_6000.rds")
+T19_8_gblup_prediction_all_6001_7297=readRDS(file="T19_8_gblup_prediction_all_6001_7297.rds")
+T19_8_gblup_prediction_all=c(T19_8_gblup_prediction_all_1_1000,T19_8_gblup_prediction_all_1001_2000,T19_8_gblup_prediction_all_2001_3000,T19_8_gblup_prediction_all_3001_4000,T19_8_gblup_prediction_all_4001_5000,T19_8_gblup_prediction_all_5001_6000,T19_8_gblup_prediction_all_6001_7297)
+
+T19_8_gblup_variances_all_1_1000=readRDS(file="T19_8_gblup_variances_all_1_1000.rds")
+T19_8_gblup_variances_all_1001_2000=readRDS(file="T19_8_gblup_variances_all_1001_2000.rds")
+T19_8_gblup_variances_all_2001_3000=readRDS(file="T19_8_gblup_variances_all_2001_3000.rds")
+T19_8_gblup_variances_all_3001_4000=readRDS(file="T19_8_gblup_variances_all_3001_4000.rds")
+T19_8_gblup_variances_all_4001_5000=readRDS(file="T19_8_gblup_variances_all_4001_5000.rds")
+T19_8_gblup_variances_all_5001_6000=readRDS(file="T19_8_gblup_variances_all_5001_6000.rds")
+T19_8_gblup_variances_all_6001_7297=readRDS(file="T19_8_gblup_variances_all_6001_7297.rds")
+T19_8_gblup_variances_all=c(T19_8_gblup_variances_all_1_1000,T19_8_gblup_variances_all_1001_2000,T19_8_gblup_variances_all_2001_3000,T19_8_gblup_variances_all_3001_4000,T19_8_gblup_variances_all_4001_5000,T19_8_gblup_variances_all_5001_6000,T19_8_gblup_variances_all_6001_7297)
+
+saveRDS(T19_8_gblup_prediction_all,"T19_8_gblup_prediction_all.rds")
+saveRDS(T19_8_gblup_variances_all,"T19_8_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T19_8_gfblup_prediction_all_1_1000=readRDS(file="T19_8_gfblup_prediction_all_1_1000.rds")
+T19_8_gfblup_prediction_all_1001_2000=readRDS(file="T19_8_gfblup_prediction_all_1001_2000.rds")
+T19_8_gfblup_prediction_all_2001_3000=readRDS(file="T19_8_gfblup_prediction_all_2001_3000.rds")
+T19_8_gfblup_prediction_all_3001_4000=readRDS(file="T19_8_gfblup_prediction_all_3001_4000.rds")
+T19_8_gfblup_prediction_all_4001_5000=readRDS(file="T19_8_gfblup_prediction_all_4001_5000.rds")
+T19_8_gfblup_prediction_all_5001_6000=readRDS(file="T19_8_gfblup_prediction_all_5001_6000.rds")
+T19_8_gfblup_prediction_all_6001_7297=readRDS(file="T19_8_gfblup_prediction_all_6001_7297.rds")
+
+T19_8_gfblup_variances_all_1_1000=readRDS(file="T19_8_gfblup_variances_all_1_1000.rds")
+T19_8_gfblup_variances_all_1001_2000=readRDS(file="T19_8_gfblup_variances_all_1001_2000.rds")
+T19_8_gfblup_variances_all_2001_3000=readRDS(file="T19_8_gfblup_variances_all_2001_3000.rds")
+T19_8_gfblup_variances_all_3001_4000=readRDS(file="T19_8_gfblup_variances_all_3001_4000.rds")
+T19_8_gfblup_variances_all_4001_5000=readRDS(file="T19_8_gfblup_variances_all_4001_5000.rds")
+T19_8_gfblup_variances_all_5001_6000=readRDS(file="T19_8_gfblup_variances_all_5001_6000.rds")
+T19_8_gfblup_variances_all_6001_7297=readRDS(file="T19_8_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T19_8_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T19_8_gfblup_variances_all=rep(list(list()),cycles)
+T19_8_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_1_1000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_1001_2000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_2001_3000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_3001_4000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_4001_5000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_5001_6000[[r]])
+	T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_6001_7297[[r]])
+
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_1_1000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_1001_2000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_2001_3000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_3001_4000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_4001_5000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_5001_6000[[r]])
+	T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T19_8_gfblup_prediction_all,"T19_8_gfblup_prediction_all.rds")
+saveRDS(T19_8_gfblup_variances_all,"T19_8_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T20_1_gblup_prediction_all_1_1000=readRDS(file="T20_1_gblup_prediction_all_1_1000.rds")
+T20_1_gblup_prediction_all_1001_2000=readRDS(file="T20_1_gblup_prediction_all_1001_2000.rds")
+T20_1_gblup_prediction_all_2001_3000=readRDS(file="T20_1_gblup_prediction_all_2001_3000.rds")
+T20_1_gblup_prediction_all_3001_4000=readRDS(file="T20_1_gblup_prediction_all_3001_4000.rds")
+T20_1_gblup_prediction_all_4001_5000=readRDS(file="T20_1_gblup_prediction_all_4001_5000.rds")
+T20_1_gblup_prediction_all_5001_6000=readRDS(file="T20_1_gblup_prediction_all_5001_6000.rds")
+T20_1_gblup_prediction_all_6001_7297=readRDS(file="T20_1_gblup_prediction_all_6001_7297.rds")
+T20_1_gblup_prediction_all=c(T20_1_gblup_prediction_all_1_1000,T20_1_gblup_prediction_all_1001_2000,T20_1_gblup_prediction_all_2001_3000,T20_1_gblup_prediction_all_3001_4000,T20_1_gblup_prediction_all_4001_5000,T20_1_gblup_prediction_all_5001_6000,T20_1_gblup_prediction_all_6001_7297)
+
+T20_1_gblup_variances_all_1_1000=readRDS(file="T20_1_gblup_variances_all_1_1000.rds")
+T20_1_gblup_variances_all_1001_2000=readRDS(file="T20_1_gblup_variances_all_1001_2000.rds")
+T20_1_gblup_variances_all_2001_3000=readRDS(file="T20_1_gblup_variances_all_2001_3000.rds")
+T20_1_gblup_variances_all_3001_4000=readRDS(file="T20_1_gblup_variances_all_3001_4000.rds")
+T20_1_gblup_variances_all_4001_5000=readRDS(file="T20_1_gblup_variances_all_4001_5000.rds")
+T20_1_gblup_variances_all_5001_6000=readRDS(file="T20_1_gblup_variances_all_5001_6000.rds")
+T20_1_gblup_variances_all_6001_7297=readRDS(file="T20_1_gblup_variances_all_6001_7297.rds")
+T20_1_gblup_variances_all=c(T20_1_gblup_variances_all_1_1000,T20_1_gblup_variances_all_1001_2000,T20_1_gblup_variances_all_2001_3000,T20_1_gblup_variances_all_3001_4000,T20_1_gblup_variances_all_4001_5000,T20_1_gblup_variances_all_5001_6000,T20_1_gblup_variances_all_6001_7297)
+
+saveRDS(T20_1_gblup_prediction_all,"T20_1_gblup_prediction_all.rds")
+saveRDS(T20_1_gblup_variances_all,"T20_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T20_1_gfblup_prediction_all_1_1000=readRDS(file="T20_1_gfblup_prediction_all_1_1000.rds")
+T20_1_gfblup_prediction_all_1001_2000=readRDS(file="T20_1_gfblup_prediction_all_1001_2000.rds")
+T20_1_gfblup_prediction_all_2001_3000=readRDS(file="T20_1_gfblup_prediction_all_2001_3000.rds")
+T20_1_gfblup_prediction_all_3001_4000=readRDS(file="T20_1_gfblup_prediction_all_3001_4000.rds")
+T20_1_gfblup_prediction_all_4001_5000=readRDS(file="T20_1_gfblup_prediction_all_4001_5000.rds")
+T20_1_gfblup_prediction_all_5001_6000=readRDS(file="T20_1_gfblup_prediction_all_5001_6000.rds")
+T20_1_gfblup_prediction_all_6001_7297=readRDS(file="T20_1_gfblup_prediction_all_6001_7297.rds")
+
+T20_1_gfblup_variances_all_1_1000=readRDS(file="T20_1_gfblup_variances_all_1_1000.rds")
+T20_1_gfblup_variances_all_1001_2000=readRDS(file="T20_1_gfblup_variances_all_1001_2000.rds")
+T20_1_gfblup_variances_all_2001_3000=readRDS(file="T20_1_gfblup_variances_all_2001_3000.rds")
+T20_1_gfblup_variances_all_3001_4000=readRDS(file="T20_1_gfblup_variances_all_3001_4000.rds")
+T20_1_gfblup_variances_all_4001_5000=readRDS(file="T20_1_gfblup_variances_all_4001_5000.rds")
+T20_1_gfblup_variances_all_5001_6000=readRDS(file="T20_1_gfblup_variances_all_5001_6000.rds")
+T20_1_gfblup_variances_all_6001_7297=readRDS(file="T20_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T20_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T20_1_gfblup_variances_all=rep(list(list()),cycles)
+T20_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_1_1000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_1001_2000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_2001_3000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_3001_4000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_4001_5000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_5001_6000[[r]])
+	T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_6001_7297[[r]])
+
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_1_1000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_1001_2000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_2001_3000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_3001_4000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_4001_5000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_5001_6000[[r]])
+	T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T20_1_gfblup_prediction_all,"T20_1_gfblup_prediction_all.rds")
+saveRDS(T20_1_gfblup_variances_all,"T20_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T20_2_gblup_prediction_all_1_1000=readRDS(file="T20_2_gblup_prediction_all_1_1000.rds")
+T20_2_gblup_prediction_all_1001_2000=readRDS(file="T20_2_gblup_prediction_all_1001_2000.rds")
+T20_2_gblup_prediction_all_2001_3000=readRDS(file="T20_2_gblup_prediction_all_2001_3000.rds")
+T20_2_gblup_prediction_all_3001_4000=readRDS(file="T20_2_gblup_prediction_all_3001_4000.rds")
+T20_2_gblup_prediction_all_4001_5000=readRDS(file="T20_2_gblup_prediction_all_4001_5000.rds")
+T20_2_gblup_prediction_all_5001_6000=readRDS(file="T20_2_gblup_prediction_all_5001_6000.rds")
+T20_2_gblup_prediction_all_6001_7297=readRDS(file="T20_2_gblup_prediction_all_6001_7297.rds")
+T20_2_gblup_prediction_all=c(T20_2_gblup_prediction_all_1_1000,T20_2_gblup_prediction_all_1001_2000,T20_2_gblup_prediction_all_2001_3000,T20_2_gblup_prediction_all_3001_4000,T20_2_gblup_prediction_all_4001_5000,T20_2_gblup_prediction_all_5001_6000,T20_2_gblup_prediction_all_6001_7297)
+
+T20_2_gblup_variances_all_1_1000=readRDS(file="T20_2_gblup_variances_all_1_1000.rds")
+T20_2_gblup_variances_all_1001_2000=readRDS(file="T20_2_gblup_variances_all_1001_2000.rds")
+T20_2_gblup_variances_all_2001_3000=readRDS(file="T20_2_gblup_variances_all_2001_3000.rds")
+T20_2_gblup_variances_all_3001_4000=readRDS(file="T20_2_gblup_variances_all_3001_4000.rds")
+T20_2_gblup_variances_all_4001_5000=readRDS(file="T20_2_gblup_variances_all_4001_5000.rds")
+T20_2_gblup_variances_all_5001_6000=readRDS(file="T20_2_gblup_variances_all_5001_6000.rds")
+T20_2_gblup_variances_all_6001_7297=readRDS(file="T20_2_gblup_variances_all_6001_7297.rds")
+T20_2_gblup_variances_all=c(T20_2_gblup_variances_all_1_1000,T20_2_gblup_variances_all_1001_2000,T20_2_gblup_variances_all_2001_3000,T20_2_gblup_variances_all_3001_4000,T20_2_gblup_variances_all_4001_5000,T20_2_gblup_variances_all_5001_6000,T20_2_gblup_variances_all_6001_7297)
+
+saveRDS(T20_2_gblup_prediction_all,"T20_2_gblup_prediction_all.rds")
+saveRDS(T20_2_gblup_variances_all,"T20_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+T20_2_gfblup_prediction_all_1_1000=readRDS(file="T20_2_gfblup_prediction_all_1_1000.rds")
+T20_2_gfblup_prediction_all_1001_2000=readRDS(file="T20_2_gfblup_prediction_all_1001_2000.rds")
+T20_2_gfblup_prediction_all_2001_3000=readRDS(file="T20_2_gfblup_prediction_all_2001_3000.rds")
+T20_2_gfblup_prediction_all_3001_4000=readRDS(file="T20_2_gfblup_prediction_all_3001_4000.rds")
+T20_2_gfblup_prediction_all_4001_5000=readRDS(file="T20_2_gfblup_prediction_all_4001_5000.rds")
+T20_2_gfblup_prediction_all_5001_6000=readRDS(file="T20_2_gfblup_prediction_all_5001_6000.rds")
+T20_2_gfblup_prediction_all_6001_7297=readRDS(file="T20_2_gfblup_prediction_all_6001_7297.rds")
+
+T20_2_gfblup_variances_all_1_1000=readRDS(file="T20_2_gfblup_variances_all_1_1000.rds")
+T20_2_gfblup_variances_all_1001_2000=readRDS(file="T20_2_gfblup_variances_all_1001_2000.rds")
+T20_2_gfblup_variances_all_2001_3000=readRDS(file="T20_2_gfblup_variances_all_2001_3000.rds")
+T20_2_gfblup_variances_all_3001_4000=readRDS(file="T20_2_gfblup_variances_all_3001_4000.rds")
+T20_2_gfblup_variances_all_4001_5000=readRDS(file="T20_2_gfblup_variances_all_4001_5000.rds")
+T20_2_gfblup_variances_all_5001_6000=readRDS(file="T20_2_gfblup_variances_all_5001_6000.rds")
+T20_2_gfblup_variances_all_6001_7297=readRDS(file="T20_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(T20_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+T20_2_gfblup_variances_all=rep(list(list()),cycles)
+T20_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_1_1000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_1001_2000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_2001_3000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_3001_4000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_4001_5000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_5001_6000[[r]])
+	T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_6001_7297[[r]])
+
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_1_1000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_1001_2000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_2001_3000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_3001_4000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_4001_5000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_5001_6000[[r]])
+	T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(T20_2_gfblup_prediction_all,"T20_2_gfblup_prediction_all.rds")
+saveRDS(T20_2_gfblup_variances_all,"T20_2_gfblup_variances_all.rds")
+
diff --git a/code/using_GO/pla/T14_1_1001_2000.R b/code/using_GO/pla/T14_1_1001_2000.R
index 5e317bd..76efe84 100644
--- a/code/using_GO/pla/T14_1_1001_2000.R
+++ b/code/using_GO/pla/T14_1_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000]
 rGF_filtered<-rGF_filtered[1001:2000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_1_1_1000.R b/code/using_GO/pla/T14_1_1_1000.R
index 9516a0f..403c8bd 100644
--- a/code/using_GO/pla/T14_1_1_1000.R
+++ b/code/using_GO/pla/T14_1_1_1000.R
@@ -7,9 +7,25 @@ is.installed <- function(mypkg)
     is.element(mypkg, installed.packages()[,1])
 } 
 ########################################################################################
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
-
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 #if (!is.installed("backports"))
 #{
 #  install.packages("backports")
@@ -32,26 +48,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +78,7 @@ GF_filtered<-GF_filtered[1:1000]
 rGF_filtered<-rGF_filtered[1:1000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_1_2001_3000.R b/code/using_GO/pla/T14_1_2001_3000.R
index 2313921..e2b6874 100644
--- a/code/using_GO/pla/T14_1_2001_3000.R
+++ b/code/using_GO/pla/T14_1_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000]
 rGF_filtered<-rGF_filtered[2001:3000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_1_3001_4000.R b/code/using_GO/pla/T14_1_3001_4000.R
index 8ac39a5..9a40589 100644
--- a/code/using_GO/pla/T14_1_3001_4000.R
+++ b/code/using_GO/pla/T14_1_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000]
 rGF_filtered<-rGF_filtered[3001:4000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_1_4001_5000.R b/code/using_GO/pla/T14_1_4001_5000.R
index 3e47124..81ca77f 100644
--- a/code/using_GO/pla/T14_1_4001_5000.R
+++ b/code/using_GO/pla/T14_1_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000]
 rGF_filtered<-rGF_filtered[4001:5000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_1_5001_6000.R b/code/using_GO/pla/T14_1_5001_6000.R
index eeed787..4c4debc 100644
--- a/code/using_GO/pla/T14_1_5001_6000.R
+++ b/code/using_GO/pla/T14_1_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000]
 rGF_filtered<-rGF_filtered[5001:6000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_1_6001_7297.R b/code/using_GO/pla/T14_1_6001_7297.R
index 7697a44..b00fe79 100644
--- a/code/using_GO/pla/T14_1_6001_7297.R
+++ b/code/using_GO/pla/T14_1_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297]
 rGF_filtered<-rGF_filtered[6001:7297]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_2_1001_2000.R b/code/using_GO/pla/T14_2_1001_2000.R
index 5a11ab6..fc02a47 100644
--- a/code/using_GO/pla/T14_2_1001_2000.R
+++ b/code/using_GO/pla/T14_2_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000]
 rGF_filtered<-rGF_filtered[1001:2000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_2_1_1000.R b/code/using_GO/pla/T14_2_1_1000.R
index e4d1021..be9ef7e 100644
--- a/code/using_GO/pla/T14_2_1_1000.R
+++ b/code/using_GO/pla/T14_2_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000]
 rGF_filtered<-rGF_filtered[1:1000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_2_2001_3000.R b/code/using_GO/pla/T14_2_2001_3000.R
index f1414c6..74c9f92 100644
--- a/code/using_GO/pla/T14_2_2001_3000.R
+++ b/code/using_GO/pla/T14_2_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000]
 rGF_filtered<-rGF_filtered[2001:3000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_2_3001_4000.R b/code/using_GO/pla/T14_2_3001_4000.R
index ae553ea..0ad0b08 100644
--- a/code/using_GO/pla/T14_2_3001_4000.R
+++ b/code/using_GO/pla/T14_2_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000]
 rGF_filtered<-rGF_filtered[3001:4000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_2_4001_5000.R b/code/using_GO/pla/T14_2_4001_5000.R
index 97de7ee..331d3c9 100644
--- a/code/using_GO/pla/T14_2_4001_5000.R
+++ b/code/using_GO/pla/T14_2_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000]
 rGF_filtered<-rGF_filtered[4001:5000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_2_5001_6000.R b/code/using_GO/pla/T14_2_5001_6000.R
index fc38029..118bdf2 100644
--- a/code/using_GO/pla/T14_2_5001_6000.R
+++ b/code/using_GO/pla/T14_2_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000]
 rGF_filtered<-rGF_filtered[5001:6000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_2_6001_7297.R b/code/using_GO/pla/T14_2_6001_7297.R
index 1e2fb34..23065af 100644
--- a/code/using_GO/pla/T14_2_6001_7297.R
+++ b/code/using_GO/pla/T14_2_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297]
 rGF_filtered<-rGF_filtered[6001:7297]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_3_1001_2000.R b/code/using_GO/pla/T14_3_1001_2000.R
index d39f3ac..f323f91 100644
--- a/code/using_GO/pla/T14_3_1001_2000.R
+++ b/code/using_GO/pla/T14_3_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000]
 rGF_filtered<-rGF_filtered[1001:2000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_3_1_1000.R b/code/using_GO/pla/T14_3_1_1000.R
index e88f5c0..4a66d73 100644
--- a/code/using_GO/pla/T14_3_1_1000.R
+++ b/code/using_GO/pla/T14_3_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000]
 rGF_filtered<-rGF_filtered[1:1000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_3_2001_3000.R b/code/using_GO/pla/T14_3_2001_3000.R
index 151fff0..8711683 100644
--- a/code/using_GO/pla/T14_3_2001_3000.R
+++ b/code/using_GO/pla/T14_3_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000]
 rGF_filtered<-rGF_filtered[2001:3000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_3_3001_4000.R b/code/using_GO/pla/T14_3_3001_4000.R
index 8cc719c..93b77d9 100644
--- a/code/using_GO/pla/T14_3_3001_4000.R
+++ b/code/using_GO/pla/T14_3_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000]
 rGF_filtered<-rGF_filtered[3001:4000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_3_4001_5000.R b/code/using_GO/pla/T14_3_4001_5000.R
index 7100d15..4a37308 100644
--- a/code/using_GO/pla/T14_3_4001_5000.R
+++ b/code/using_GO/pla/T14_3_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000]
 rGF_filtered<-rGF_filtered[4001:5000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_3_5001_6000.R b/code/using_GO/pla/T14_3_5001_6000.R
index 26e941c..233ff21 100644
--- a/code/using_GO/pla/T14_3_5001_6000.R
+++ b/code/using_GO/pla/T14_3_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000]
 rGF_filtered<-rGF_filtered[5001:6000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_3_6001_7297.R b/code/using_GO/pla/T14_3_6001_7297.R
index 9130398..4b4c77e 100644
--- a/code/using_GO/pla/T14_3_6001_7297.R
+++ b/code/using_GO/pla/T14_3_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297]
 rGF_filtered<-rGF_filtered[6001:7297]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_4_1001_2000.R b/code/using_GO/pla/T14_4_1001_2000.R
index 3e4419d..4168ad3 100644
--- a/code/using_GO/pla/T14_4_1001_2000.R
+++ b/code/using_GO/pla/T14_4_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000]
 rGF_filtered<-rGF_filtered[1001:2000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_4_1_1000.R b/code/using_GO/pla/T14_4_1_1000.R
index fb82682..dcd8e92 100644
--- a/code/using_GO/pla/T14_4_1_1000.R
+++ b/code/using_GO/pla/T14_4_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000]
 rGF_filtered<-rGF_filtered[1:1000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_4_2001_3000.R b/code/using_GO/pla/T14_4_2001_3000.R
index 6bd2e0b..7af88f5 100644
--- a/code/using_GO/pla/T14_4_2001_3000.R
+++ b/code/using_GO/pla/T14_4_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000]
 rGF_filtered<-rGF_filtered[2001:3000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_4_3001_4000.R b/code/using_GO/pla/T14_4_3001_4000.R
index 7ab7605..2e82b0a 100644
--- a/code/using_GO/pla/T14_4_3001_4000.R
+++ b/code/using_GO/pla/T14_4_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000]
 rGF_filtered<-rGF_filtered[3001:4000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_4_4001_5000.R b/code/using_GO/pla/T14_4_4001_5000.R
index 5a05ccb..d81659e 100644
--- a/code/using_GO/pla/T14_4_4001_5000.R
+++ b/code/using_GO/pla/T14_4_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000]
 rGF_filtered<-rGF_filtered[4001:5000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_4_5001_6000.R b/code/using_GO/pla/T14_4_5001_6000.R
index 8a992cf..a493ada 100644
--- a/code/using_GO/pla/T14_4_5001_6000.R
+++ b/code/using_GO/pla/T14_4_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000]
 rGF_filtered<-rGF_filtered[5001:6000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_4_6001_7297.R b/code/using_GO/pla/T14_4_6001_7297.R
index 0c0e0e5..4fd17e2 100644
--- a/code/using_GO/pla/T14_4_6001_7297.R
+++ b/code/using_GO/pla/T14_4_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297]
 rGF_filtered<-rGF_filtered[6001:7297]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_5_1001_2000.R b/code/using_GO/pla/T14_5_1001_2000.R
index 6f75e58..3b71ca4 100644
--- a/code/using_GO/pla/T14_5_1001_2000.R
+++ b/code/using_GO/pla/T14_5_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000]
 rGF_filtered<-rGF_filtered[1001:2000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_5_1_1000.R b/code/using_GO/pla/T14_5_1_1000.R
index 6118957..214e6c3 100644
--- a/code/using_GO/pla/T14_5_1_1000.R
+++ b/code/using_GO/pla/T14_5_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000]
 rGF_filtered<-rGF_filtered[1:1000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_5_2001_3000.R b/code/using_GO/pla/T14_5_2001_3000.R
index a5b4328..2239b92 100644
--- a/code/using_GO/pla/T14_5_2001_3000.R
+++ b/code/using_GO/pla/T14_5_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000]
 rGF_filtered<-rGF_filtered[2001:3000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_5_3001_4000.R b/code/using_GO/pla/T14_5_3001_4000.R
index 87343d1..fca111e 100644
--- a/code/using_GO/pla/T14_5_3001_4000.R
+++ b/code/using_GO/pla/T14_5_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000]
 rGF_filtered<-rGF_filtered[3001:4000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_5_4001_5000.R b/code/using_GO/pla/T14_5_4001_5000.R
index a43c6db..eb00f67 100644
--- a/code/using_GO/pla/T14_5_4001_5000.R
+++ b/code/using_GO/pla/T14_5_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000]
 rGF_filtered<-rGF_filtered[4001:5000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_5_5001_6000.R b/code/using_GO/pla/T14_5_5001_6000.R
index d6df895..7de5864 100644
--- a/code/using_GO/pla/T14_5_5001_6000.R
+++ b/code/using_GO/pla/T14_5_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000]
 rGF_filtered<-rGF_filtered[5001:6000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_5_6001_7297.R b/code/using_GO/pla/T14_5_6001_7297.R
index 4308141..a0d7956 100644
--- a/code/using_GO/pla/T14_5_6001_7297.R
+++ b/code/using_GO/pla/T14_5_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297]
 rGF_filtered<-rGF_filtered[6001:7297]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_6_1001_2000.R b/code/using_GO/pla/T14_6_1001_2000.R
index 615caa4..86e67e3 100644
--- a/code/using_GO/pla/T14_6_1001_2000.R
+++ b/code/using_GO/pla/T14_6_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000]
 rGF_filtered<-rGF_filtered[1001:2000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_6_1_1000.R b/code/using_GO/pla/T14_6_1_1000.R
index 49aa03e..3b1a8c1 100644
--- a/code/using_GO/pla/T14_6_1_1000.R
+++ b/code/using_GO/pla/T14_6_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000]
 rGF_filtered<-rGF_filtered[1:1000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_6_2001_3000.R b/code/using_GO/pla/T14_6_2001_3000.R
index c6cbc4c..45c9f76 100644
--- a/code/using_GO/pla/T14_6_2001_3000.R
+++ b/code/using_GO/pla/T14_6_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000]
 rGF_filtered<-rGF_filtered[2001:3000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_6_3001_4000.R b/code/using_GO/pla/T14_6_3001_4000.R
index 6fa0004..53208ca 100644
--- a/code/using_GO/pla/T14_6_3001_4000.R
+++ b/code/using_GO/pla/T14_6_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000]
 rGF_filtered<-rGF_filtered[3001:4000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_6_4001_5000.R b/code/using_GO/pla/T14_6_4001_5000.R
index 5ff2b56..1c2b54e 100644
--- a/code/using_GO/pla/T14_6_4001_5000.R
+++ b/code/using_GO/pla/T14_6_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000]
 rGF_filtered<-rGF_filtered[4001:5000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_6_5001_6000.R b/code/using_GO/pla/T14_6_5001_6000.R
index e9bc5e0..d9d2f5d 100644
--- a/code/using_GO/pla/T14_6_5001_6000.R
+++ b/code/using_GO/pla/T14_6_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000]
 rGF_filtered<-rGF_filtered[5001:6000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_6_6001_7297.R b/code/using_GO/pla/T14_6_6001_7297.R
index c3c71cc..9f23b4e 100644
--- a/code/using_GO/pla/T14_6_6001_7297.R
+++ b/code/using_GO/pla/T14_6_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297]
 rGF_filtered<-rGF_filtered[6001:7297]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_7_1001_2000.R b/code/using_GO/pla/T14_7_1001_2000.R
index fb02a3a..c634197 100644
--- a/code/using_GO/pla/T14_7_1001_2000.R
+++ b/code/using_GO/pla/T14_7_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000]
 rGF_filtered<-rGF_filtered[1001:2000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_7_1_1000.R b/code/using_GO/pla/T14_7_1_1000.R
index 56d9307..3544e74 100644
--- a/code/using_GO/pla/T14_7_1_1000.R
+++ b/code/using_GO/pla/T14_7_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000]
 rGF_filtered<-rGF_filtered[1:1000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_7_2001_3000.R b/code/using_GO/pla/T14_7_2001_3000.R
index ec3844f..73c0600 100644
--- a/code/using_GO/pla/T14_7_2001_3000.R
+++ b/code/using_GO/pla/T14_7_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000]
 rGF_filtered<-rGF_filtered[2001:3000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_7_3001_4000.R b/code/using_GO/pla/T14_7_3001_4000.R
index 59ca235..a3de9fb 100644
--- a/code/using_GO/pla/T14_7_3001_4000.R
+++ b/code/using_GO/pla/T14_7_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000]
 rGF_filtered<-rGF_filtered[3001:4000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_7_4001_5000.R b/code/using_GO/pla/T14_7_4001_5000.R
index a9742f2..975a04f 100644
--- a/code/using_GO/pla/T14_7_4001_5000.R
+++ b/code/using_GO/pla/T14_7_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000]
 rGF_filtered<-rGF_filtered[4001:5000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_7_5001_6000.R b/code/using_GO/pla/T14_7_5001_6000.R
index 2a794aa..d25c511 100644
--- a/code/using_GO/pla/T14_7_5001_6000.R
+++ b/code/using_GO/pla/T14_7_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000]
 rGF_filtered<-rGF_filtered[5001:6000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_7_6001_7297.R b/code/using_GO/pla/T14_7_6001_7297.R
index 378da97..3a3a18d 100644
--- a/code/using_GO/pla/T14_7_6001_7297.R
+++ b/code/using_GO/pla/T14_7_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297]
 rGF_filtered<-rGF_filtered[6001:7297]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_8_1001_2000.R b/code/using_GO/pla/T14_8_1001_2000.R
index 2b24837..bbfb37e 100644
--- a/code/using_GO/pla/T14_8_1001_2000.R
+++ b/code/using_GO/pla/T14_8_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000]
 rGF_filtered<-rGF_filtered[1001:2000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_8_1_1000.R b/code/using_GO/pla/T14_8_1_1000.R
index 7c10b96..71896ad 100644
--- a/code/using_GO/pla/T14_8_1_1000.R
+++ b/code/using_GO/pla/T14_8_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000]
 rGF_filtered<-rGF_filtered[1:1000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_8_2001_3000.R b/code/using_GO/pla/T14_8_2001_3000.R
index 723ac35..ea91644 100644
--- a/code/using_GO/pla/T14_8_2001_3000.R
+++ b/code/using_GO/pla/T14_8_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000]
 rGF_filtered<-rGF_filtered[2001:3000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_8_3001_4000.R b/code/using_GO/pla/T14_8_3001_4000.R
index 5d2d962..85697e5 100644
--- a/code/using_GO/pla/T14_8_3001_4000.R
+++ b/code/using_GO/pla/T14_8_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000]
 rGF_filtered<-rGF_filtered[3001:4000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_8_4001_5000.R b/code/using_GO/pla/T14_8_4001_5000.R
index 0000231..9be86c0 100644
--- a/code/using_GO/pla/T14_8_4001_5000.R
+++ b/code/using_GO/pla/T14_8_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000]
 rGF_filtered<-rGF_filtered[4001:5000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_8_5001_6000.R b/code/using_GO/pla/T14_8_5001_6000.R
index ff599fc..16f0677 100644
--- a/code/using_GO/pla/T14_8_5001_6000.R
+++ b/code/using_GO/pla/T14_8_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000]
 rGF_filtered<-rGF_filtered[5001:6000]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T14_8_6001_7297.R b/code/using_GO/pla/T14_8_6001_7297.R
index 3a0790d..98dabdf 100644
--- a/code/using_GO/pla/T14_8_6001_7297.R
+++ b/code/using_GO/pla/T14_8_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297]
 rGF_filtered<-rGF_filtered[6001:7297]
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T14_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_1_1001_2000.R b/code/using_GO/pla/T15_1_1001_2000.R
index 3906677..79d3f61 100644
--- a/code/using_GO/pla/T15_1_1001_2000.R
+++ b/code/using_GO/pla/T15_1_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_1_1_1000.R b/code/using_GO/pla/T15_1_1_1000.R
index 461709b..96fa54a 100644
--- a/code/using_GO/pla/T15_1_1_1000.R
+++ b/code/using_GO/pla/T15_1_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_1_2001_3000.R b/code/using_GO/pla/T15_1_2001_3000.R
index ef4eac4..7eb18f5 100644
--- a/code/using_GO/pla/T15_1_2001_3000.R
+++ b/code/using_GO/pla/T15_1_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_1_3001_4000.R b/code/using_GO/pla/T15_1_3001_4000.R
index 3a101f1..73535a6 100644
--- a/code/using_GO/pla/T15_1_3001_4000.R
+++ b/code/using_GO/pla/T15_1_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_1_4001_5000.R b/code/using_GO/pla/T15_1_4001_5000.R
index 8258197..10ca074 100644
--- a/code/using_GO/pla/T15_1_4001_5000.R
+++ b/code/using_GO/pla/T15_1_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_1_5001_6000.R b/code/using_GO/pla/T15_1_5001_6000.R
index d5998cf..2b0d451 100644
--- a/code/using_GO/pla/T15_1_5001_6000.R
+++ b/code/using_GO/pla/T15_1_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_1_6001_7297.R b/code/using_GO/pla/T15_1_6001_7297.R
index 27cae6a..dfe215a 100644
--- a/code/using_GO/pla/T15_1_6001_7297.R
+++ b/code/using_GO/pla/T15_1_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_2_1001_2000.R b/code/using_GO/pla/T15_2_1001_2000.R
index 708769f..71dd7c7 100644
--- a/code/using_GO/pla/T15_2_1001_2000.R
+++ b/code/using_GO/pla/T15_2_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_2_1_1000.R b/code/using_GO/pla/T15_2_1_1000.R
index 05caeeb..d321b2b 100644
--- a/code/using_GO/pla/T15_2_1_1000.R
+++ b/code/using_GO/pla/T15_2_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_2_2001_3000.R b/code/using_GO/pla/T15_2_2001_3000.R
index defc899..234cf08 100644
--- a/code/using_GO/pla/T15_2_2001_3000.R
+++ b/code/using_GO/pla/T15_2_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_2_3001_4000.R b/code/using_GO/pla/T15_2_3001_4000.R
index 4eac70c..18bcb38 100644
--- a/code/using_GO/pla/T15_2_3001_4000.R
+++ b/code/using_GO/pla/T15_2_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_2_4001_5000.R b/code/using_GO/pla/T15_2_4001_5000.R
index fbac682..ed9f208 100644
--- a/code/using_GO/pla/T15_2_4001_5000.R
+++ b/code/using_GO/pla/T15_2_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_2_5001_6000.R b/code/using_GO/pla/T15_2_5001_6000.R
index 37ee8d4..452ba5c 100644
--- a/code/using_GO/pla/T15_2_5001_6000.R
+++ b/code/using_GO/pla/T15_2_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_2_6001_7297.R b/code/using_GO/pla/T15_2_6001_7297.R
index 036845f..6337c5c 100644
--- a/code/using_GO/pla/T15_2_6001_7297.R
+++ b/code/using_GO/pla/T15_2_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_3_1001_2000.R b/code/using_GO/pla/T15_3_1001_2000.R
index 022bfcc..0df2773 100644
--- a/code/using_GO/pla/T15_3_1001_2000.R
+++ b/code/using_GO/pla/T15_3_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_3_1_1000.R b/code/using_GO/pla/T15_3_1_1000.R
index 28741e3..21bd8ee 100644
--- a/code/using_GO/pla/T15_3_1_1000.R
+++ b/code/using_GO/pla/T15_3_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_3_2001_3000.R b/code/using_GO/pla/T15_3_2001_3000.R
index 06b102d..e3aba60 100644
--- a/code/using_GO/pla/T15_3_2001_3000.R
+++ b/code/using_GO/pla/T15_3_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_3_3001_4000.R b/code/using_GO/pla/T15_3_3001_4000.R
index 24a12e5..71e8c19 100644
--- a/code/using_GO/pla/T15_3_3001_4000.R
+++ b/code/using_GO/pla/T15_3_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_3_4001_5000.R b/code/using_GO/pla/T15_3_4001_5000.R
index ab79059..9a4110e 100644
--- a/code/using_GO/pla/T15_3_4001_5000.R
+++ b/code/using_GO/pla/T15_3_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_3_5001_6000.R b/code/using_GO/pla/T15_3_5001_6000.R
index 40ca42f..ca08ede 100644
--- a/code/using_GO/pla/T15_3_5001_6000.R
+++ b/code/using_GO/pla/T15_3_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_3_6001_7297.R b/code/using_GO/pla/T15_3_6001_7297.R
index b9945bc..d1b50dd 100644
--- a/code/using_GO/pla/T15_3_6001_7297.R
+++ b/code/using_GO/pla/T15_3_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_4_1001_2000.R b/code/using_GO/pla/T15_4_1001_2000.R
index 2b4d312..78002b6 100644
--- a/code/using_GO/pla/T15_4_1001_2000.R
+++ b/code/using_GO/pla/T15_4_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_4_1_1000.R b/code/using_GO/pla/T15_4_1_1000.R
index 056cb6b..cfa5af2 100644
--- a/code/using_GO/pla/T15_4_1_1000.R
+++ b/code/using_GO/pla/T15_4_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_4_2001_3000.R b/code/using_GO/pla/T15_4_2001_3000.R
index 8e4e371..1e244f2 100644
--- a/code/using_GO/pla/T15_4_2001_3000.R
+++ b/code/using_GO/pla/T15_4_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_4_3001_4000.R b/code/using_GO/pla/T15_4_3001_4000.R
index 21bb254..d55b5cd 100644
--- a/code/using_GO/pla/T15_4_3001_4000.R
+++ b/code/using_GO/pla/T15_4_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_4_4001_5000.R b/code/using_GO/pla/T15_4_4001_5000.R
index 37fedac..532b14f 100644
--- a/code/using_GO/pla/T15_4_4001_5000.R
+++ b/code/using_GO/pla/T15_4_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_4_5001_6000.R b/code/using_GO/pla/T15_4_5001_6000.R
index 5c474ab..e8957c6 100644
--- a/code/using_GO/pla/T15_4_5001_6000.R
+++ b/code/using_GO/pla/T15_4_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_4_6001_7297.R b/code/using_GO/pla/T15_4_6001_7297.R
index 6b4e58e..d9018c3 100644
--- a/code/using_GO/pla/T15_4_6001_7297.R
+++ b/code/using_GO/pla/T15_4_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_5_1001_2000.R b/code/using_GO/pla/T15_5_1001_2000.R
index f2ffdac..db47e64 100644
--- a/code/using_GO/pla/T15_5_1001_2000.R
+++ b/code/using_GO/pla/T15_5_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_5_1_1000.R b/code/using_GO/pla/T15_5_1_1000.R
index 566bf79..3d637b3 100644
--- a/code/using_GO/pla/T15_5_1_1000.R
+++ b/code/using_GO/pla/T15_5_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_5_2001_3000.R b/code/using_GO/pla/T15_5_2001_3000.R
index d7f1909..c20aa25 100644
--- a/code/using_GO/pla/T15_5_2001_3000.R
+++ b/code/using_GO/pla/T15_5_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_5_3001_4000.R b/code/using_GO/pla/T15_5_3001_4000.R
index c4dc648..b031116 100644
--- a/code/using_GO/pla/T15_5_3001_4000.R
+++ b/code/using_GO/pla/T15_5_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_5_4001_5000.R b/code/using_GO/pla/T15_5_4001_5000.R
index 949ffc1..c7472df 100644
--- a/code/using_GO/pla/T15_5_4001_5000.R
+++ b/code/using_GO/pla/T15_5_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_5_5001_6000.R b/code/using_GO/pla/T15_5_5001_6000.R
index 49e9a78..8a8f8a5 100644
--- a/code/using_GO/pla/T15_5_5001_6000.R
+++ b/code/using_GO/pla/T15_5_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_5_6001_7297.R b/code/using_GO/pla/T15_5_6001_7297.R
index e93c701..1fa2d54 100644
--- a/code/using_GO/pla/T15_5_6001_7297.R
+++ b/code/using_GO/pla/T15_5_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_6_1001_2000.R b/code/using_GO/pla/T15_6_1001_2000.R
index 6e615e7..b1a51a0 100644
--- a/code/using_GO/pla/T15_6_1001_2000.R
+++ b/code/using_GO/pla/T15_6_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_6_1_1000.R b/code/using_GO/pla/T15_6_1_1000.R
index c302bb2..85b8efc 100644
--- a/code/using_GO/pla/T15_6_1_1000.R
+++ b/code/using_GO/pla/T15_6_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_6_2001_3000.R b/code/using_GO/pla/T15_6_2001_3000.R
index 36197e0..c5b57bd 100644
--- a/code/using_GO/pla/T15_6_2001_3000.R
+++ b/code/using_GO/pla/T15_6_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_6_3001_4000.R b/code/using_GO/pla/T15_6_3001_4000.R
index 42c1875..446cb3f 100644
--- a/code/using_GO/pla/T15_6_3001_4000.R
+++ b/code/using_GO/pla/T15_6_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_6_4001_5000.R b/code/using_GO/pla/T15_6_4001_5000.R
index 760db50..5d4ed08 100644
--- a/code/using_GO/pla/T15_6_4001_5000.R
+++ b/code/using_GO/pla/T15_6_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_6_5001_6000.R b/code/using_GO/pla/T15_6_5001_6000.R
index b23f2ac..5114d92 100644
--- a/code/using_GO/pla/T15_6_5001_6000.R
+++ b/code/using_GO/pla/T15_6_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_6_6001_7297.R b/code/using_GO/pla/T15_6_6001_7297.R
index 78c2aee..96e8c78 100644
--- a/code/using_GO/pla/T15_6_6001_7297.R
+++ b/code/using_GO/pla/T15_6_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_7_1001_2000.R b/code/using_GO/pla/T15_7_1001_2000.R
index c0786b9..2a39ba2 100644
--- a/code/using_GO/pla/T15_7_1001_2000.R
+++ b/code/using_GO/pla/T15_7_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_7_1_1000.R b/code/using_GO/pla/T15_7_1_1000.R
index 86ba4bc..79d628a 100644
--- a/code/using_GO/pla/T15_7_1_1000.R
+++ b/code/using_GO/pla/T15_7_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_7_2001_3000.R b/code/using_GO/pla/T15_7_2001_3000.R
index 4c7d977..4655add 100644
--- a/code/using_GO/pla/T15_7_2001_3000.R
+++ b/code/using_GO/pla/T15_7_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_7_3001_4000.R b/code/using_GO/pla/T15_7_3001_4000.R
index 49a5a81..c7186ef 100644
--- a/code/using_GO/pla/T15_7_3001_4000.R
+++ b/code/using_GO/pla/T15_7_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_7_4001_5000.R b/code/using_GO/pla/T15_7_4001_5000.R
index 824c878..5696c58 100644
--- a/code/using_GO/pla/T15_7_4001_5000.R
+++ b/code/using_GO/pla/T15_7_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_7_5001_6000.R b/code/using_GO/pla/T15_7_5001_6000.R
index 92c45f8..fbb5564 100644
--- a/code/using_GO/pla/T15_7_5001_6000.R
+++ b/code/using_GO/pla/T15_7_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_7_6001_7297.R b/code/using_GO/pla/T15_7_6001_7297.R
index 58ee2a3..70658ef 100644
--- a/code/using_GO/pla/T15_7_6001_7297.R
+++ b/code/using_GO/pla/T15_7_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_8_1001_2000.R b/code/using_GO/pla/T15_8_1001_2000.R
index a903e50..1943005 100644
--- a/code/using_GO/pla/T15_8_1001_2000.R
+++ b/code/using_GO/pla/T15_8_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_8_1_1000.R b/code/using_GO/pla/T15_8_1_1000.R
index 29b7426..e8bd77b 100644
--- a/code/using_GO/pla/T15_8_1_1000.R
+++ b/code/using_GO/pla/T15_8_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_8_2001_3000.R b/code/using_GO/pla/T15_8_2001_3000.R
index 8e9ff54..3b7e215 100644
--- a/code/using_GO/pla/T15_8_2001_3000.R
+++ b/code/using_GO/pla/T15_8_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_8_3001_4000.R b/code/using_GO/pla/T15_8_3001_4000.R
index 098466e..1a9215b 100644
--- a/code/using_GO/pla/T15_8_3001_4000.R
+++ b/code/using_GO/pla/T15_8_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_8_4001_5000.R b/code/using_GO/pla/T15_8_4001_5000.R
index 8c0f44c..1123714 100644
--- a/code/using_GO/pla/T15_8_4001_5000.R
+++ b/code/using_GO/pla/T15_8_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_8_5001_6000.R b/code/using_GO/pla/T15_8_5001_6000.R
index 6b7141f..eb806fa 100644
--- a/code/using_GO/pla/T15_8_5001_6000.R
+++ b/code/using_GO/pla/T15_8_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T15_8_6001_7297.R b/code/using_GO/pla/T15_8_6001_7297.R
index 94a92df..e7ae6b4 100644
--- a/code/using_GO/pla/T15_8_6001_7297.R
+++ b/code/using_GO/pla/T15_8_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T15_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_1_1001_2000.R b/code/using_GO/pla/T16_1_1001_2000.R
index 15c58c9..87f433d 100644
--- a/code/using_GO/pla/T16_1_1001_2000.R
+++ b/code/using_GO/pla/T16_1_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_1_1_1000.R b/code/using_GO/pla/T16_1_1_1000.R
index 5859c7d..ef8a83a 100644
--- a/code/using_GO/pla/T16_1_1_1000.R
+++ b/code/using_GO/pla/T16_1_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_1_2001_3000.R b/code/using_GO/pla/T16_1_2001_3000.R
index b98a17a..5eee3a8 100644
--- a/code/using_GO/pla/T16_1_2001_3000.R
+++ b/code/using_GO/pla/T16_1_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_1_3001_4000.R b/code/using_GO/pla/T16_1_3001_4000.R
index d50b026..543b440 100644
--- a/code/using_GO/pla/T16_1_3001_4000.R
+++ b/code/using_GO/pla/T16_1_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_1_4001_5000.R b/code/using_GO/pla/T16_1_4001_5000.R
index 9b96548..383b304 100644
--- a/code/using_GO/pla/T16_1_4001_5000.R
+++ b/code/using_GO/pla/T16_1_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_1_5001_6000.R b/code/using_GO/pla/T16_1_5001_6000.R
index 8e3db7d..298fee2 100644
--- a/code/using_GO/pla/T16_1_5001_6000.R
+++ b/code/using_GO/pla/T16_1_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_1_6001_7297.R b/code/using_GO/pla/T16_1_6001_7297.R
index 136d48f..f0bfa49 100644
--- a/code/using_GO/pla/T16_1_6001_7297.R
+++ b/code/using_GO/pla/T16_1_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_2_1001_2000.R b/code/using_GO/pla/T16_2_1001_2000.R
index e7d6af6..bdcef89 100644
--- a/code/using_GO/pla/T16_2_1001_2000.R
+++ b/code/using_GO/pla/T16_2_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_2_1_1000.R b/code/using_GO/pla/T16_2_1_1000.R
index b18897d..e1c836c 100644
--- a/code/using_GO/pla/T16_2_1_1000.R
+++ b/code/using_GO/pla/T16_2_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_2_2001_3000.R b/code/using_GO/pla/T16_2_2001_3000.R
index 69c45b4..9198413 100644
--- a/code/using_GO/pla/T16_2_2001_3000.R
+++ b/code/using_GO/pla/T16_2_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_2_3001_4000.R b/code/using_GO/pla/T16_2_3001_4000.R
index 8c47046..e0a2093 100644
--- a/code/using_GO/pla/T16_2_3001_4000.R
+++ b/code/using_GO/pla/T16_2_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_2_4001_5000.R b/code/using_GO/pla/T16_2_4001_5000.R
index 78ed0a3..963d553 100644
--- a/code/using_GO/pla/T16_2_4001_5000.R
+++ b/code/using_GO/pla/T16_2_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_2_5001_6000.R b/code/using_GO/pla/T16_2_5001_6000.R
index ffb62ea..51b9d06 100644
--- a/code/using_GO/pla/T16_2_5001_6000.R
+++ b/code/using_GO/pla/T16_2_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_2_6001_7297.R b/code/using_GO/pla/T16_2_6001_7297.R
index 20f381b..e5dca94 100644
--- a/code/using_GO/pla/T16_2_6001_7297.R
+++ b/code/using_GO/pla/T16_2_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_3_1001_2000.R b/code/using_GO/pla/T16_3_1001_2000.R
index 0c2b84f..e1c2286 100644
--- a/code/using_GO/pla/T16_3_1001_2000.R
+++ b/code/using_GO/pla/T16_3_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_3_1_1000.R b/code/using_GO/pla/T16_3_1_1000.R
index 3eef118..c093d4c 100644
--- a/code/using_GO/pla/T16_3_1_1000.R
+++ b/code/using_GO/pla/T16_3_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_3_2001_3000.R b/code/using_GO/pla/T16_3_2001_3000.R
index d84db56..6bb1d82 100644
--- a/code/using_GO/pla/T16_3_2001_3000.R
+++ b/code/using_GO/pla/T16_3_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_3_3001_4000.R b/code/using_GO/pla/T16_3_3001_4000.R
index 6164a25..0b6349b 100644
--- a/code/using_GO/pla/T16_3_3001_4000.R
+++ b/code/using_GO/pla/T16_3_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_3_4001_5000.R b/code/using_GO/pla/T16_3_4001_5000.R
index 95234f4..edf0b8f 100644
--- a/code/using_GO/pla/T16_3_4001_5000.R
+++ b/code/using_GO/pla/T16_3_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_3_5001_6000.R b/code/using_GO/pla/T16_3_5001_6000.R
index 13231fc..5722cb4 100644
--- a/code/using_GO/pla/T16_3_5001_6000.R
+++ b/code/using_GO/pla/T16_3_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_3_6001_7297.R b/code/using_GO/pla/T16_3_6001_7297.R
index 9df06b4..b19bd5e 100644
--- a/code/using_GO/pla/T16_3_6001_7297.R
+++ b/code/using_GO/pla/T16_3_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_4_1001_2000.R b/code/using_GO/pla/T16_4_1001_2000.R
index e0d44ef..45c55fb 100644
--- a/code/using_GO/pla/T16_4_1001_2000.R
+++ b/code/using_GO/pla/T16_4_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_4_1_1000.R b/code/using_GO/pla/T16_4_1_1000.R
index 5cd0a6a..88c17b0 100644
--- a/code/using_GO/pla/T16_4_1_1000.R
+++ b/code/using_GO/pla/T16_4_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_4_2001_3000.R b/code/using_GO/pla/T16_4_2001_3000.R
index 0f6358c..177dff6 100644
--- a/code/using_GO/pla/T16_4_2001_3000.R
+++ b/code/using_GO/pla/T16_4_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_4_3001_4000.R b/code/using_GO/pla/T16_4_3001_4000.R
index ed80345..b38d7c7 100644
--- a/code/using_GO/pla/T16_4_3001_4000.R
+++ b/code/using_GO/pla/T16_4_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_4_4001_5000.R b/code/using_GO/pla/T16_4_4001_5000.R
index af19553..a911201 100644
--- a/code/using_GO/pla/T16_4_4001_5000.R
+++ b/code/using_GO/pla/T16_4_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_4_5001_6000.R b/code/using_GO/pla/T16_4_5001_6000.R
index 6f9695b..ccde480 100644
--- a/code/using_GO/pla/T16_4_5001_6000.R
+++ b/code/using_GO/pla/T16_4_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_4_6001_7297.R b/code/using_GO/pla/T16_4_6001_7297.R
index 83f9c5e..f4288b0 100644
--- a/code/using_GO/pla/T16_4_6001_7297.R
+++ b/code/using_GO/pla/T16_4_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_5_1001_2000.R b/code/using_GO/pla/T16_5_1001_2000.R
index ff653c6..291bcaa 100644
--- a/code/using_GO/pla/T16_5_1001_2000.R
+++ b/code/using_GO/pla/T16_5_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_5_1_1000.R b/code/using_GO/pla/T16_5_1_1000.R
index 4d3c582..e8e1922 100644
--- a/code/using_GO/pla/T16_5_1_1000.R
+++ b/code/using_GO/pla/T16_5_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_5_2001_3000.R b/code/using_GO/pla/T16_5_2001_3000.R
index 7c24bf9..370666f 100644
--- a/code/using_GO/pla/T16_5_2001_3000.R
+++ b/code/using_GO/pla/T16_5_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_5_3001_4000.R b/code/using_GO/pla/T16_5_3001_4000.R
index ca125a1..29434ef 100644
--- a/code/using_GO/pla/T16_5_3001_4000.R
+++ b/code/using_GO/pla/T16_5_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_5_4001_5000.R b/code/using_GO/pla/T16_5_4001_5000.R
index 51fb1d5..f1058c6 100644
--- a/code/using_GO/pla/T16_5_4001_5000.R
+++ b/code/using_GO/pla/T16_5_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_5_5001_6000.R b/code/using_GO/pla/T16_5_5001_6000.R
index 8c07cb0..26423fd 100644
--- a/code/using_GO/pla/T16_5_5001_6000.R
+++ b/code/using_GO/pla/T16_5_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_5_6001_7297.R b/code/using_GO/pla/T16_5_6001_7297.R
index 5f8f3a1..0c460ff 100644
--- a/code/using_GO/pla/T16_5_6001_7297.R
+++ b/code/using_GO/pla/T16_5_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_6_1001_2000.R b/code/using_GO/pla/T16_6_1001_2000.R
index fb207ad..5a4c3cb 100644
--- a/code/using_GO/pla/T16_6_1001_2000.R
+++ b/code/using_GO/pla/T16_6_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_6_1_1000.R b/code/using_GO/pla/T16_6_1_1000.R
index dcabdb7..eea5b2a 100644
--- a/code/using_GO/pla/T16_6_1_1000.R
+++ b/code/using_GO/pla/T16_6_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_6_2001_3000.R b/code/using_GO/pla/T16_6_2001_3000.R
index 8fc0e62..f56010d 100644
--- a/code/using_GO/pla/T16_6_2001_3000.R
+++ b/code/using_GO/pla/T16_6_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_6_3001_4000.R b/code/using_GO/pla/T16_6_3001_4000.R
index 38e7f57..335c918 100644
--- a/code/using_GO/pla/T16_6_3001_4000.R
+++ b/code/using_GO/pla/T16_6_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_6_4001_5000.R b/code/using_GO/pla/T16_6_4001_5000.R
index 7dd77a0..879695e 100644
--- a/code/using_GO/pla/T16_6_4001_5000.R
+++ b/code/using_GO/pla/T16_6_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_6_5001_6000.R b/code/using_GO/pla/T16_6_5001_6000.R
index 0d1b710..c460fdf 100644
--- a/code/using_GO/pla/T16_6_5001_6000.R
+++ b/code/using_GO/pla/T16_6_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_6_6001_7297.R b/code/using_GO/pla/T16_6_6001_7297.R
index 803624b..2476534 100644
--- a/code/using_GO/pla/T16_6_6001_7297.R
+++ b/code/using_GO/pla/T16_6_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_7_1001_2000.R b/code/using_GO/pla/T16_7_1001_2000.R
index a39cc0c..9da9b13 100644
--- a/code/using_GO/pla/T16_7_1001_2000.R
+++ b/code/using_GO/pla/T16_7_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_7_1_1000.R b/code/using_GO/pla/T16_7_1_1000.R
index a39d072..d4b8ccf 100644
--- a/code/using_GO/pla/T16_7_1_1000.R
+++ b/code/using_GO/pla/T16_7_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_7_2001_3000.R b/code/using_GO/pla/T16_7_2001_3000.R
index bab3ffc..4de6071 100644
--- a/code/using_GO/pla/T16_7_2001_3000.R
+++ b/code/using_GO/pla/T16_7_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_7_3001_4000.R b/code/using_GO/pla/T16_7_3001_4000.R
index 57956bd..b10199f 100644
--- a/code/using_GO/pla/T16_7_3001_4000.R
+++ b/code/using_GO/pla/T16_7_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_7_4001_5000.R b/code/using_GO/pla/T16_7_4001_5000.R
index 4316185..7001304 100644
--- a/code/using_GO/pla/T16_7_4001_5000.R
+++ b/code/using_GO/pla/T16_7_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_7_5001_6000.R b/code/using_GO/pla/T16_7_5001_6000.R
index 97b4439..3ac02ed 100644
--- a/code/using_GO/pla/T16_7_5001_6000.R
+++ b/code/using_GO/pla/T16_7_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_7_6001_7297.R b/code/using_GO/pla/T16_7_6001_7297.R
index db9166b..9f97f20 100644
--- a/code/using_GO/pla/T16_7_6001_7297.R
+++ b/code/using_GO/pla/T16_7_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_8_1001_2000.R b/code/using_GO/pla/T16_8_1001_2000.R
index 79d4a6a..8a4db13 100644
--- a/code/using_GO/pla/T16_8_1001_2000.R
+++ b/code/using_GO/pla/T16_8_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_8_1_1000.R b/code/using_GO/pla/T16_8_1_1000.R
index 781b0fa..b7b4154 100644
--- a/code/using_GO/pla/T16_8_1_1000.R
+++ b/code/using_GO/pla/T16_8_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_8_2001_3000.R b/code/using_GO/pla/T16_8_2001_3000.R
index f1a1c6c..158fff1 100644
--- a/code/using_GO/pla/T16_8_2001_3000.R
+++ b/code/using_GO/pla/T16_8_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_8_3001_4000.R b/code/using_GO/pla/T16_8_3001_4000.R
index 1969932..e7a9ed4 100644
--- a/code/using_GO/pla/T16_8_3001_4000.R
+++ b/code/using_GO/pla/T16_8_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_8_4001_5000.R b/code/using_GO/pla/T16_8_4001_5000.R
index 13cd2b5..ca097de 100644
--- a/code/using_GO/pla/T16_8_4001_5000.R
+++ b/code/using_GO/pla/T16_8_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_8_5001_6000.R b/code/using_GO/pla/T16_8_5001_6000.R
index 02ed2cb..64ec4da 100644
--- a/code/using_GO/pla/T16_8_5001_6000.R
+++ b/code/using_GO/pla/T16_8_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T16_8_6001_7297.R b/code/using_GO/pla/T16_8_6001_7297.R
index af6422c..de02610 100644
--- a/code/using_GO/pla/T16_8_6001_7297.R
+++ b/code/using_GO/pla/T16_8_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T16_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_1_1001_2000.R b/code/using_GO/pla/T17_1_1001_2000.R
index 4d1f06a..96285d7 100644
--- a/code/using_GO/pla/T17_1_1001_2000.R
+++ b/code/using_GO/pla/T17_1_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_1_1_1000.R b/code/using_GO/pla/T17_1_1_1000.R
index f1828d5..766237a 100644
--- a/code/using_GO/pla/T17_1_1_1000.R
+++ b/code/using_GO/pla/T17_1_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_1_2001_3000.R b/code/using_GO/pla/T17_1_2001_3000.R
index 3fa741e..45fe912 100644
--- a/code/using_GO/pla/T17_1_2001_3000.R
+++ b/code/using_GO/pla/T17_1_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_1_3001_4000.R b/code/using_GO/pla/T17_1_3001_4000.R
index c780745..9aaa571 100644
--- a/code/using_GO/pla/T17_1_3001_4000.R
+++ b/code/using_GO/pla/T17_1_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_1_4001_5000.R b/code/using_GO/pla/T17_1_4001_5000.R
index b21d591..052c104 100644
--- a/code/using_GO/pla/T17_1_4001_5000.R
+++ b/code/using_GO/pla/T17_1_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_1_5001_6000.R b/code/using_GO/pla/T17_1_5001_6000.R
index d3b15f2..6672414 100644
--- a/code/using_GO/pla/T17_1_5001_6000.R
+++ b/code/using_GO/pla/T17_1_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_1_6001_7297.R b/code/using_GO/pla/T17_1_6001_7297.R
index d99c215..ecfd9bd 100644
--- a/code/using_GO/pla/T17_1_6001_7297.R
+++ b/code/using_GO/pla/T17_1_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_2_1001_2000.R b/code/using_GO/pla/T17_2_1001_2000.R
index c9ab357..20f7f48 100644
--- a/code/using_GO/pla/T17_2_1001_2000.R
+++ b/code/using_GO/pla/T17_2_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_2_1_1000.R b/code/using_GO/pla/T17_2_1_1000.R
index 21c3638..b96ef0e 100644
--- a/code/using_GO/pla/T17_2_1_1000.R
+++ b/code/using_GO/pla/T17_2_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_2_2001_3000.R b/code/using_GO/pla/T17_2_2001_3000.R
index 1b5235f..5c50053 100644
--- a/code/using_GO/pla/T17_2_2001_3000.R
+++ b/code/using_GO/pla/T17_2_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_2_3001_4000.R b/code/using_GO/pla/T17_2_3001_4000.R
index 9bb7650..471cb6f 100644
--- a/code/using_GO/pla/T17_2_3001_4000.R
+++ b/code/using_GO/pla/T17_2_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_2_4001_5000.R b/code/using_GO/pla/T17_2_4001_5000.R
index 9bc8e48..2ab0401 100644
--- a/code/using_GO/pla/T17_2_4001_5000.R
+++ b/code/using_GO/pla/T17_2_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_2_5001_6000.R b/code/using_GO/pla/T17_2_5001_6000.R
index d83851d..a8da5fa 100644
--- a/code/using_GO/pla/T17_2_5001_6000.R
+++ b/code/using_GO/pla/T17_2_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_2_6001_7297.R b/code/using_GO/pla/T17_2_6001_7297.R
index d39f74a..be45dd3 100644
--- a/code/using_GO/pla/T17_2_6001_7297.R
+++ b/code/using_GO/pla/T17_2_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_3_1001_2000.R b/code/using_GO/pla/T17_3_1001_2000.R
index 92fb346..e91dea6 100644
--- a/code/using_GO/pla/T17_3_1001_2000.R
+++ b/code/using_GO/pla/T17_3_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_3_1_1000.R b/code/using_GO/pla/T17_3_1_1000.R
index dd3f119..4d67879 100644
--- a/code/using_GO/pla/T17_3_1_1000.R
+++ b/code/using_GO/pla/T17_3_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_3_2001_3000.R b/code/using_GO/pla/T17_3_2001_3000.R
index 5896ef5..74154a0 100644
--- a/code/using_GO/pla/T17_3_2001_3000.R
+++ b/code/using_GO/pla/T17_3_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_3_3001_4000.R b/code/using_GO/pla/T17_3_3001_4000.R
index d0e95d1..2e6035a 100644
--- a/code/using_GO/pla/T17_3_3001_4000.R
+++ b/code/using_GO/pla/T17_3_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_3_4001_5000.R b/code/using_GO/pla/T17_3_4001_5000.R
index bf5c72d..6a74a7b 100644
--- a/code/using_GO/pla/T17_3_4001_5000.R
+++ b/code/using_GO/pla/T17_3_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_3_5001_6000.R b/code/using_GO/pla/T17_3_5001_6000.R
index 5a87115..2ff4120 100644
--- a/code/using_GO/pla/T17_3_5001_6000.R
+++ b/code/using_GO/pla/T17_3_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_3_6001_7297.R b/code/using_GO/pla/T17_3_6001_7297.R
index e8732e5..6ba5d85 100644
--- a/code/using_GO/pla/T17_3_6001_7297.R
+++ b/code/using_GO/pla/T17_3_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_4_1001_2000.R b/code/using_GO/pla/T17_4_1001_2000.R
index 19cd99b..9f0778f 100644
--- a/code/using_GO/pla/T17_4_1001_2000.R
+++ b/code/using_GO/pla/T17_4_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_4_1_1000.R b/code/using_GO/pla/T17_4_1_1000.R
index cc87926..bc5c859 100644
--- a/code/using_GO/pla/T17_4_1_1000.R
+++ b/code/using_GO/pla/T17_4_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_4_2001_3000.R b/code/using_GO/pla/T17_4_2001_3000.R
index 5eb4e62..4624372 100644
--- a/code/using_GO/pla/T17_4_2001_3000.R
+++ b/code/using_GO/pla/T17_4_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_4_3001_4000.R b/code/using_GO/pla/T17_4_3001_4000.R
index edf1dfb..861ef2c 100644
--- a/code/using_GO/pla/T17_4_3001_4000.R
+++ b/code/using_GO/pla/T17_4_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_4_4001_5000.R b/code/using_GO/pla/T17_4_4001_5000.R
index 9f1b98f..c9b79c0 100644
--- a/code/using_GO/pla/T17_4_4001_5000.R
+++ b/code/using_GO/pla/T17_4_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_4_5001_6000.R b/code/using_GO/pla/T17_4_5001_6000.R
index d3f9d0a..549b5d6 100644
--- a/code/using_GO/pla/T17_4_5001_6000.R
+++ b/code/using_GO/pla/T17_4_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_4_6001_7297.R b/code/using_GO/pla/T17_4_6001_7297.R
index b773a9c..dc72a19 100644
--- a/code/using_GO/pla/T17_4_6001_7297.R
+++ b/code/using_GO/pla/T17_4_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_5_1001_2000.R b/code/using_GO/pla/T17_5_1001_2000.R
index 6adad76..51ec6e8 100644
--- a/code/using_GO/pla/T17_5_1001_2000.R
+++ b/code/using_GO/pla/T17_5_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_5_1_1000.R b/code/using_GO/pla/T17_5_1_1000.R
index d423904..3948b76 100644
--- a/code/using_GO/pla/T17_5_1_1000.R
+++ b/code/using_GO/pla/T17_5_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_5_2001_3000.R b/code/using_GO/pla/T17_5_2001_3000.R
index 365c4ca..84cd259 100644
--- a/code/using_GO/pla/T17_5_2001_3000.R
+++ b/code/using_GO/pla/T17_5_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_5_3001_4000.R b/code/using_GO/pla/T17_5_3001_4000.R
index 5a70ee4..8368d79 100644
--- a/code/using_GO/pla/T17_5_3001_4000.R
+++ b/code/using_GO/pla/T17_5_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_5_4001_5000.R b/code/using_GO/pla/T17_5_4001_5000.R
index fbd7400..2831d3b 100644
--- a/code/using_GO/pla/T17_5_4001_5000.R
+++ b/code/using_GO/pla/T17_5_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_5_5001_6000.R b/code/using_GO/pla/T17_5_5001_6000.R
index f6d90f2..32d59de 100644
--- a/code/using_GO/pla/T17_5_5001_6000.R
+++ b/code/using_GO/pla/T17_5_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_5_6001_7297.R b/code/using_GO/pla/T17_5_6001_7297.R
index 94e5775..2158e86 100644
--- a/code/using_GO/pla/T17_5_6001_7297.R
+++ b/code/using_GO/pla/T17_5_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_6_1001_2000.R b/code/using_GO/pla/T17_6_1001_2000.R
index 6c041cd..56e99b6 100644
--- a/code/using_GO/pla/T17_6_1001_2000.R
+++ b/code/using_GO/pla/T17_6_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_6_1_1000.R b/code/using_GO/pla/T17_6_1_1000.R
index 46860ae..004148e 100644
--- a/code/using_GO/pla/T17_6_1_1000.R
+++ b/code/using_GO/pla/T17_6_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_6_2001_3000.R b/code/using_GO/pla/T17_6_2001_3000.R
index 41e9f52..09fc419 100644
--- a/code/using_GO/pla/T17_6_2001_3000.R
+++ b/code/using_GO/pla/T17_6_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_6_3001_4000.R b/code/using_GO/pla/T17_6_3001_4000.R
index 165d60b..295532f 100644
--- a/code/using_GO/pla/T17_6_3001_4000.R
+++ b/code/using_GO/pla/T17_6_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_6_4001_5000.R b/code/using_GO/pla/T17_6_4001_5000.R
index abe1608..15a3fe1 100644
--- a/code/using_GO/pla/T17_6_4001_5000.R
+++ b/code/using_GO/pla/T17_6_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_6_5001_6000.R b/code/using_GO/pla/T17_6_5001_6000.R
index 96c1530..84cedac 100644
--- a/code/using_GO/pla/T17_6_5001_6000.R
+++ b/code/using_GO/pla/T17_6_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_6_6001_7297.R b/code/using_GO/pla/T17_6_6001_7297.R
index f21d37b..2d5c201 100644
--- a/code/using_GO/pla/T17_6_6001_7297.R
+++ b/code/using_GO/pla/T17_6_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_7_1001_2000.R b/code/using_GO/pla/T17_7_1001_2000.R
index 0482886..376a81f 100644
--- a/code/using_GO/pla/T17_7_1001_2000.R
+++ b/code/using_GO/pla/T17_7_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_7_1_1000.R b/code/using_GO/pla/T17_7_1_1000.R
index bfcf41e..a4ace90 100644
--- a/code/using_GO/pla/T17_7_1_1000.R
+++ b/code/using_GO/pla/T17_7_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_7_2001_3000.R b/code/using_GO/pla/T17_7_2001_3000.R
index 732e7ff..3290f13 100644
--- a/code/using_GO/pla/T17_7_2001_3000.R
+++ b/code/using_GO/pla/T17_7_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_7_3001_4000.R b/code/using_GO/pla/T17_7_3001_4000.R
index 9903532..0aaf4d1 100644
--- a/code/using_GO/pla/T17_7_3001_4000.R
+++ b/code/using_GO/pla/T17_7_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_7_4001_5000.R b/code/using_GO/pla/T17_7_4001_5000.R
index cf0bd60..4619e5f 100644
--- a/code/using_GO/pla/T17_7_4001_5000.R
+++ b/code/using_GO/pla/T17_7_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_7_5001_6000.R b/code/using_GO/pla/T17_7_5001_6000.R
index 7ea3049..39e4cb6 100644
--- a/code/using_GO/pla/T17_7_5001_6000.R
+++ b/code/using_GO/pla/T17_7_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_7_6001_7297.R b/code/using_GO/pla/T17_7_6001_7297.R
index aeda6a2..b4ce0fe 100644
--- a/code/using_GO/pla/T17_7_6001_7297.R
+++ b/code/using_GO/pla/T17_7_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_8_1001_2000.R b/code/using_GO/pla/T17_8_1001_2000.R
index 4484afb..8d49cce 100644
--- a/code/using_GO/pla/T17_8_1001_2000.R
+++ b/code/using_GO/pla/T17_8_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_8_1_1000.R b/code/using_GO/pla/T17_8_1_1000.R
index 17ff577..c530429 100644
--- a/code/using_GO/pla/T17_8_1_1000.R
+++ b/code/using_GO/pla/T17_8_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_8_2001_3000.R b/code/using_GO/pla/T17_8_2001_3000.R
index d35a28b..957b532 100644
--- a/code/using_GO/pla/T17_8_2001_3000.R
+++ b/code/using_GO/pla/T17_8_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_8_3001_4000.R b/code/using_GO/pla/T17_8_3001_4000.R
index 97ac630..52f95be 100644
--- a/code/using_GO/pla/T17_8_3001_4000.R
+++ b/code/using_GO/pla/T17_8_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_8_4001_5000.R b/code/using_GO/pla/T17_8_4001_5000.R
index 343dbb0..656a0cf 100644
--- a/code/using_GO/pla/T17_8_4001_5000.R
+++ b/code/using_GO/pla/T17_8_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_8_5001_6000.R b/code/using_GO/pla/T17_8_5001_6000.R
index 0cef780..6b1bb26 100644
--- a/code/using_GO/pla/T17_8_5001_6000.R
+++ b/code/using_GO/pla/T17_8_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T17_8_6001_7297.R b/code/using_GO/pla/T17_8_6001_7297.R
index a433111..e422447 100644
--- a/code/using_GO/pla/T17_8_6001_7297.R
+++ b/code/using_GO/pla/T17_8_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T17_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_1_1001_2000.R b/code/using_GO/pla/T18_1_1001_2000.R
index e395a94..3d15255 100644
--- a/code/using_GO/pla/T18_1_1001_2000.R
+++ b/code/using_GO/pla/T18_1_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_1_1_1000.R b/code/using_GO/pla/T18_1_1_1000.R
index aa48c3c..1984618 100644
--- a/code/using_GO/pla/T18_1_1_1000.R
+++ b/code/using_GO/pla/T18_1_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_1_2001_3000.R b/code/using_GO/pla/T18_1_2001_3000.R
index 8cc1b22..eec0015 100644
--- a/code/using_GO/pla/T18_1_2001_3000.R
+++ b/code/using_GO/pla/T18_1_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_1_3001_4000.R b/code/using_GO/pla/T18_1_3001_4000.R
index bbd0e59..81459db 100644
--- a/code/using_GO/pla/T18_1_3001_4000.R
+++ b/code/using_GO/pla/T18_1_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_1_4001_5000.R b/code/using_GO/pla/T18_1_4001_5000.R
index 0020d41..3c367ff 100644
--- a/code/using_GO/pla/T18_1_4001_5000.R
+++ b/code/using_GO/pla/T18_1_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_1_5001_6000.R b/code/using_GO/pla/T18_1_5001_6000.R
index 21fb218..ce134bb 100644
--- a/code/using_GO/pla/T18_1_5001_6000.R
+++ b/code/using_GO/pla/T18_1_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_1_6001_7297.R b/code/using_GO/pla/T18_1_6001_7297.R
index f9bbf65..409c3eb 100644
--- a/code/using_GO/pla/T18_1_6001_7297.R
+++ b/code/using_GO/pla/T18_1_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_2_1001_2000.R b/code/using_GO/pla/T18_2_1001_2000.R
index 49d5979..3a1a699 100644
--- a/code/using_GO/pla/T18_2_1001_2000.R
+++ b/code/using_GO/pla/T18_2_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_2_1_1000.R b/code/using_GO/pla/T18_2_1_1000.R
index a33fe9d..7ec0f92 100644
--- a/code/using_GO/pla/T18_2_1_1000.R
+++ b/code/using_GO/pla/T18_2_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_2_2001_3000.R b/code/using_GO/pla/T18_2_2001_3000.R
index b69edc8..cd1d13e 100644
--- a/code/using_GO/pla/T18_2_2001_3000.R
+++ b/code/using_GO/pla/T18_2_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_2_3001_4000.R b/code/using_GO/pla/T18_2_3001_4000.R
index a29a303..e82c87b 100644
--- a/code/using_GO/pla/T18_2_3001_4000.R
+++ b/code/using_GO/pla/T18_2_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_2_4001_5000.R b/code/using_GO/pla/T18_2_4001_5000.R
index 239fdb6..a379f08 100644
--- a/code/using_GO/pla/T18_2_4001_5000.R
+++ b/code/using_GO/pla/T18_2_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_2_5001_6000.R b/code/using_GO/pla/T18_2_5001_6000.R
index 95143f4..078e020 100644
--- a/code/using_GO/pla/T18_2_5001_6000.R
+++ b/code/using_GO/pla/T18_2_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_2_6001_7297.R b/code/using_GO/pla/T18_2_6001_7297.R
index 8d7216d..b352c2f 100644
--- a/code/using_GO/pla/T18_2_6001_7297.R
+++ b/code/using_GO/pla/T18_2_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_3_1001_2000.R b/code/using_GO/pla/T18_3_1001_2000.R
index 5e541d7..7267804 100644
--- a/code/using_GO/pla/T18_3_1001_2000.R
+++ b/code/using_GO/pla/T18_3_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_3_1_1000.R b/code/using_GO/pla/T18_3_1_1000.R
index 5a28208..4c135b8 100644
--- a/code/using_GO/pla/T18_3_1_1000.R
+++ b/code/using_GO/pla/T18_3_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_3_2001_3000.R b/code/using_GO/pla/T18_3_2001_3000.R
index d1d57df..0e14976 100644
--- a/code/using_GO/pla/T18_3_2001_3000.R
+++ b/code/using_GO/pla/T18_3_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_3_3001_4000.R b/code/using_GO/pla/T18_3_3001_4000.R
index 7209106..387fcf7 100644
--- a/code/using_GO/pla/T18_3_3001_4000.R
+++ b/code/using_GO/pla/T18_3_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_3_4001_5000.R b/code/using_GO/pla/T18_3_4001_5000.R
index 600b5b1..abc2365 100644
--- a/code/using_GO/pla/T18_3_4001_5000.R
+++ b/code/using_GO/pla/T18_3_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_3_5001_6000.R b/code/using_GO/pla/T18_3_5001_6000.R
index dddf977..27cd698 100644
--- a/code/using_GO/pla/T18_3_5001_6000.R
+++ b/code/using_GO/pla/T18_3_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_3_6001_7297.R b/code/using_GO/pla/T18_3_6001_7297.R
index b2ad2eb..f54c0d9 100644
--- a/code/using_GO/pla/T18_3_6001_7297.R
+++ b/code/using_GO/pla/T18_3_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_4_1001_2000.R b/code/using_GO/pla/T18_4_1001_2000.R
index f3f2b96..55a008c 100644
--- a/code/using_GO/pla/T18_4_1001_2000.R
+++ b/code/using_GO/pla/T18_4_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_4_1_1000.R b/code/using_GO/pla/T18_4_1_1000.R
index 287f784..3fa26c6 100644
--- a/code/using_GO/pla/T18_4_1_1000.R
+++ b/code/using_GO/pla/T18_4_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_4_2001_3000.R b/code/using_GO/pla/T18_4_2001_3000.R
index c6212a6..e7befd5 100644
--- a/code/using_GO/pla/T18_4_2001_3000.R
+++ b/code/using_GO/pla/T18_4_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_4_3001_4000.R b/code/using_GO/pla/T18_4_3001_4000.R
index 33598de..84beee8 100644
--- a/code/using_GO/pla/T18_4_3001_4000.R
+++ b/code/using_GO/pla/T18_4_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_4_4001_5000.R b/code/using_GO/pla/T18_4_4001_5000.R
index 1dbce5c..c5affc9 100644
--- a/code/using_GO/pla/T18_4_4001_5000.R
+++ b/code/using_GO/pla/T18_4_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_4_5001_6000.R b/code/using_GO/pla/T18_4_5001_6000.R
index ec1a8a0..d1d82bd 100644
--- a/code/using_GO/pla/T18_4_5001_6000.R
+++ b/code/using_GO/pla/T18_4_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_4_6001_7297.R b/code/using_GO/pla/T18_4_6001_7297.R
index 3827199..0fdc010 100644
--- a/code/using_GO/pla/T18_4_6001_7297.R
+++ b/code/using_GO/pla/T18_4_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_5_1001_2000.R b/code/using_GO/pla/T18_5_1001_2000.R
index 26fcb78..235a3d8 100644
--- a/code/using_GO/pla/T18_5_1001_2000.R
+++ b/code/using_GO/pla/T18_5_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_5_1_1000.R b/code/using_GO/pla/T18_5_1_1000.R
index 0a36077..599c702 100644
--- a/code/using_GO/pla/T18_5_1_1000.R
+++ b/code/using_GO/pla/T18_5_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_5_2001_3000.R b/code/using_GO/pla/T18_5_2001_3000.R
index 29dead9..f2743ff 100644
--- a/code/using_GO/pla/T18_5_2001_3000.R
+++ b/code/using_GO/pla/T18_5_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_5_3001_4000.R b/code/using_GO/pla/T18_5_3001_4000.R
index 4b7e1ad..ad4ecf8 100644
--- a/code/using_GO/pla/T18_5_3001_4000.R
+++ b/code/using_GO/pla/T18_5_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_5_4001_5000.R b/code/using_GO/pla/T18_5_4001_5000.R
index 97e3b41..3b2d3b6 100644
--- a/code/using_GO/pla/T18_5_4001_5000.R
+++ b/code/using_GO/pla/T18_5_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_5_5001_6000.R b/code/using_GO/pla/T18_5_5001_6000.R
index 7983d5c..3f7d951 100644
--- a/code/using_GO/pla/T18_5_5001_6000.R
+++ b/code/using_GO/pla/T18_5_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_5_6001_7297.R b/code/using_GO/pla/T18_5_6001_7297.R
index e086244..33a8aa9 100644
--- a/code/using_GO/pla/T18_5_6001_7297.R
+++ b/code/using_GO/pla/T18_5_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_6_1001_2000.R b/code/using_GO/pla/T18_6_1001_2000.R
index 19a770a..8b11dbe 100644
--- a/code/using_GO/pla/T18_6_1001_2000.R
+++ b/code/using_GO/pla/T18_6_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_6_1_1000.R b/code/using_GO/pla/T18_6_1_1000.R
index 5793c29..59dc1e9 100644
--- a/code/using_GO/pla/T18_6_1_1000.R
+++ b/code/using_GO/pla/T18_6_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_6_2001_3000.R b/code/using_GO/pla/T18_6_2001_3000.R
index dc17a9e..19682ac 100644
--- a/code/using_GO/pla/T18_6_2001_3000.R
+++ b/code/using_GO/pla/T18_6_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_6_3001_4000.R b/code/using_GO/pla/T18_6_3001_4000.R
index 7c305d4..f7dba2e 100644
--- a/code/using_GO/pla/T18_6_3001_4000.R
+++ b/code/using_GO/pla/T18_6_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_6_4001_5000.R b/code/using_GO/pla/T18_6_4001_5000.R
index fd400b7..52e7348 100644
--- a/code/using_GO/pla/T18_6_4001_5000.R
+++ b/code/using_GO/pla/T18_6_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_6_5001_6000.R b/code/using_GO/pla/T18_6_5001_6000.R
index 6016036..93cd5c5 100644
--- a/code/using_GO/pla/T18_6_5001_6000.R
+++ b/code/using_GO/pla/T18_6_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_6_6001_7297.R b/code/using_GO/pla/T18_6_6001_7297.R
index 32ed667..718cbd1 100644
--- a/code/using_GO/pla/T18_6_6001_7297.R
+++ b/code/using_GO/pla/T18_6_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_7_1001_2000.R b/code/using_GO/pla/T18_7_1001_2000.R
index 12d6413..1236569 100644
--- a/code/using_GO/pla/T18_7_1001_2000.R
+++ b/code/using_GO/pla/T18_7_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_7_1_1000.R b/code/using_GO/pla/T18_7_1_1000.R
index 160483d..5b2dc02 100644
--- a/code/using_GO/pla/T18_7_1_1000.R
+++ b/code/using_GO/pla/T18_7_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_7_2001_3000.R b/code/using_GO/pla/T18_7_2001_3000.R
index 8a73255..499fe04 100644
--- a/code/using_GO/pla/T18_7_2001_3000.R
+++ b/code/using_GO/pla/T18_7_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_7_3001_4000.R b/code/using_GO/pla/T18_7_3001_4000.R
index 24a77c8..9be5a1f 100644
--- a/code/using_GO/pla/T18_7_3001_4000.R
+++ b/code/using_GO/pla/T18_7_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_7_4001_5000.R b/code/using_GO/pla/T18_7_4001_5000.R
index eb76ec9..1e805e3 100644
--- a/code/using_GO/pla/T18_7_4001_5000.R
+++ b/code/using_GO/pla/T18_7_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_7_5001_6000.R b/code/using_GO/pla/T18_7_5001_6000.R
index eb898ff..10bea6c 100644
--- a/code/using_GO/pla/T18_7_5001_6000.R
+++ b/code/using_GO/pla/T18_7_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_7_6001_7297.R b/code/using_GO/pla/T18_7_6001_7297.R
index 8d9de36..a7c8db8 100644
--- a/code/using_GO/pla/T18_7_6001_7297.R
+++ b/code/using_GO/pla/T18_7_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_8_1001_2000.R b/code/using_GO/pla/T18_8_1001_2000.R
index 198b007..cf9db30 100644
--- a/code/using_GO/pla/T18_8_1001_2000.R
+++ b/code/using_GO/pla/T18_8_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_8_1_1000.R b/code/using_GO/pla/T18_8_1_1000.R
index bce9d22..5d77d1f 100644
--- a/code/using_GO/pla/T18_8_1_1000.R
+++ b/code/using_GO/pla/T18_8_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_8_2001_3000.R b/code/using_GO/pla/T18_8_2001_3000.R
index 6272077..d21531a 100644
--- a/code/using_GO/pla/T18_8_2001_3000.R
+++ b/code/using_GO/pla/T18_8_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_8_3001_4000.R b/code/using_GO/pla/T18_8_3001_4000.R
index 5f09c03..43bd8fd 100644
--- a/code/using_GO/pla/T18_8_3001_4000.R
+++ b/code/using_GO/pla/T18_8_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_8_4001_5000.R b/code/using_GO/pla/T18_8_4001_5000.R
index 9b870c8..d5dd96d 100644
--- a/code/using_GO/pla/T18_8_4001_5000.R
+++ b/code/using_GO/pla/T18_8_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_8_5001_6000.R b/code/using_GO/pla/T18_8_5001_6000.R
index efe52ac..9e29a3d 100644
--- a/code/using_GO/pla/T18_8_5001_6000.R
+++ b/code/using_GO/pla/T18_8_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T18_8_6001_7297.R b/code/using_GO/pla/T18_8_6001_7297.R
index e91b2ed..83c1e61 100644
--- a/code/using_GO/pla/T18_8_6001_7297.R
+++ b/code/using_GO/pla/T18_8_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T18_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_1_1001_2000.R b/code/using_GO/pla/T19_1_1001_2000.R
index a24d3bd..4012789 100644
--- a/code/using_GO/pla/T19_1_1001_2000.R
+++ b/code/using_GO/pla/T19_1_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_1_1_1000.R b/code/using_GO/pla/T19_1_1_1000.R
index df74bb6..075cdb9 100644
--- a/code/using_GO/pla/T19_1_1_1000.R
+++ b/code/using_GO/pla/T19_1_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_1_2001_3000.R b/code/using_GO/pla/T19_1_2001_3000.R
index 9993149..53ba190 100644
--- a/code/using_GO/pla/T19_1_2001_3000.R
+++ b/code/using_GO/pla/T19_1_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_1_3001_4000.R b/code/using_GO/pla/T19_1_3001_4000.R
index 3acc5e8..83b4677 100644
--- a/code/using_GO/pla/T19_1_3001_4000.R
+++ b/code/using_GO/pla/T19_1_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_1_4001_5000.R b/code/using_GO/pla/T19_1_4001_5000.R
index c1f7390..b153928 100644
--- a/code/using_GO/pla/T19_1_4001_5000.R
+++ b/code/using_GO/pla/T19_1_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_1_5001_6000.R b/code/using_GO/pla/T19_1_5001_6000.R
index 43fe40c..635bff5 100644
--- a/code/using_GO/pla/T19_1_5001_6000.R
+++ b/code/using_GO/pla/T19_1_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_1_6001_7297.R b/code/using_GO/pla/T19_1_6001_7297.R
index b5653ad..d0fb5c1 100644
--- a/code/using_GO/pla/T19_1_6001_7297.R
+++ b/code/using_GO/pla/T19_1_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_2_1001_2000.R b/code/using_GO/pla/T19_2_1001_2000.R
index 32966c1..eb9a0e1 100644
--- a/code/using_GO/pla/T19_2_1001_2000.R
+++ b/code/using_GO/pla/T19_2_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_2_1_1000.R b/code/using_GO/pla/T19_2_1_1000.R
index 6921cb1..a96c3f0 100644
--- a/code/using_GO/pla/T19_2_1_1000.R
+++ b/code/using_GO/pla/T19_2_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_2_2001_3000.R b/code/using_GO/pla/T19_2_2001_3000.R
index dd72470..d3710a7 100644
--- a/code/using_GO/pla/T19_2_2001_3000.R
+++ b/code/using_GO/pla/T19_2_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_2_3001_4000.R b/code/using_GO/pla/T19_2_3001_4000.R
index 37815c8..c7fae60 100644
--- a/code/using_GO/pla/T19_2_3001_4000.R
+++ b/code/using_GO/pla/T19_2_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_2_4001_5000.R b/code/using_GO/pla/T19_2_4001_5000.R
index 086a394..f6ff6a5 100644
--- a/code/using_GO/pla/T19_2_4001_5000.R
+++ b/code/using_GO/pla/T19_2_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_2_5001_6000.R b/code/using_GO/pla/T19_2_5001_6000.R
index 7633b44..fccf2f7 100644
--- a/code/using_GO/pla/T19_2_5001_6000.R
+++ b/code/using_GO/pla/T19_2_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_2_6001_7297.R b/code/using_GO/pla/T19_2_6001_7297.R
index 76fed4e..a2af490 100644
--- a/code/using_GO/pla/T19_2_6001_7297.R
+++ b/code/using_GO/pla/T19_2_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_3_1001_2000.R b/code/using_GO/pla/T19_3_1001_2000.R
index 157a4b4..fbd925c 100644
--- a/code/using_GO/pla/T19_3_1001_2000.R
+++ b/code/using_GO/pla/T19_3_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_3_1_1000.R b/code/using_GO/pla/T19_3_1_1000.R
index 692b823..aefa6e7 100644
--- a/code/using_GO/pla/T19_3_1_1000.R
+++ b/code/using_GO/pla/T19_3_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_3_2001_3000.R b/code/using_GO/pla/T19_3_2001_3000.R
index 8962a1d..9199651 100644
--- a/code/using_GO/pla/T19_3_2001_3000.R
+++ b/code/using_GO/pla/T19_3_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_3_3001_4000.R b/code/using_GO/pla/T19_3_3001_4000.R
index e09750c..d2d86f3 100644
--- a/code/using_GO/pla/T19_3_3001_4000.R
+++ b/code/using_GO/pla/T19_3_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_3_4001_5000.R b/code/using_GO/pla/T19_3_4001_5000.R
index 8daf777..0138bc7 100644
--- a/code/using_GO/pla/T19_3_4001_5000.R
+++ b/code/using_GO/pla/T19_3_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_3_5001_6000.R b/code/using_GO/pla/T19_3_5001_6000.R
index 4305ce8..54d5b56 100644
--- a/code/using_GO/pla/T19_3_5001_6000.R
+++ b/code/using_GO/pla/T19_3_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_3_6001_7297.R b/code/using_GO/pla/T19_3_6001_7297.R
index ade8f19..57b0788 100644
--- a/code/using_GO/pla/T19_3_6001_7297.R
+++ b/code/using_GO/pla/T19_3_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_3_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_4_1001_2000.R b/code/using_GO/pla/T19_4_1001_2000.R
index afebbb4..8b04bd9 100644
--- a/code/using_GO/pla/T19_4_1001_2000.R
+++ b/code/using_GO/pla/T19_4_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_4_1_1000.R b/code/using_GO/pla/T19_4_1_1000.R
index 2e215a5..51503d0 100644
--- a/code/using_GO/pla/T19_4_1_1000.R
+++ b/code/using_GO/pla/T19_4_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_4_2001_3000.R b/code/using_GO/pla/T19_4_2001_3000.R
index 729ace8..349dc21 100644
--- a/code/using_GO/pla/T19_4_2001_3000.R
+++ b/code/using_GO/pla/T19_4_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_4_3001_4000.R b/code/using_GO/pla/T19_4_3001_4000.R
index 6bf9e07..79ac4e9 100644
--- a/code/using_GO/pla/T19_4_3001_4000.R
+++ b/code/using_GO/pla/T19_4_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_4_4001_5000.R b/code/using_GO/pla/T19_4_4001_5000.R
index 5686a5e..6870955 100644
--- a/code/using_GO/pla/T19_4_4001_5000.R
+++ b/code/using_GO/pla/T19_4_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_4_5001_6000.R b/code/using_GO/pla/T19_4_5001_6000.R
index 5917ed4..c894e02 100644
--- a/code/using_GO/pla/T19_4_5001_6000.R
+++ b/code/using_GO/pla/T19_4_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_4_6001_7297.R b/code/using_GO/pla/T19_4_6001_7297.R
index 8157130..721057e 100644
--- a/code/using_GO/pla/T19_4_6001_7297.R
+++ b/code/using_GO/pla/T19_4_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_4_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_5_1001_2000.R b/code/using_GO/pla/T19_5_1001_2000.R
index d45a199..edae8dd 100644
--- a/code/using_GO/pla/T19_5_1001_2000.R
+++ b/code/using_GO/pla/T19_5_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_5_1_1000.R b/code/using_GO/pla/T19_5_1_1000.R
index f5ff7ca..a9d8923 100644
--- a/code/using_GO/pla/T19_5_1_1000.R
+++ b/code/using_GO/pla/T19_5_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_5_2001_3000.R b/code/using_GO/pla/T19_5_2001_3000.R
index 357aafd..0e693b4 100644
--- a/code/using_GO/pla/T19_5_2001_3000.R
+++ b/code/using_GO/pla/T19_5_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_5_3001_4000.R b/code/using_GO/pla/T19_5_3001_4000.R
index 8d1ab5c..2af97cd 100644
--- a/code/using_GO/pla/T19_5_3001_4000.R
+++ b/code/using_GO/pla/T19_5_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_5_4001_5000.R b/code/using_GO/pla/T19_5_4001_5000.R
index af4cb87..a62ddf3 100644
--- a/code/using_GO/pla/T19_5_4001_5000.R
+++ b/code/using_GO/pla/T19_5_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_5_5001_6000.R b/code/using_GO/pla/T19_5_5001_6000.R
index 3c1a372..aa285dc 100644
--- a/code/using_GO/pla/T19_5_5001_6000.R
+++ b/code/using_GO/pla/T19_5_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_5_6001_7297.R b/code/using_GO/pla/T19_5_6001_7297.R
index f6970db..283aa3a 100644
--- a/code/using_GO/pla/T19_5_6001_7297.R
+++ b/code/using_GO/pla/T19_5_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_5_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_6_1001_2000.R b/code/using_GO/pla/T19_6_1001_2000.R
index 0b6396c..9c4755f 100644
--- a/code/using_GO/pla/T19_6_1001_2000.R
+++ b/code/using_GO/pla/T19_6_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_6_1_1000.R b/code/using_GO/pla/T19_6_1_1000.R
index 4962934..fe92f7d 100644
--- a/code/using_GO/pla/T19_6_1_1000.R
+++ b/code/using_GO/pla/T19_6_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_6_2001_3000.R b/code/using_GO/pla/T19_6_2001_3000.R
index e89602d..49091aa 100644
--- a/code/using_GO/pla/T19_6_2001_3000.R
+++ b/code/using_GO/pla/T19_6_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_6_3001_4000.R b/code/using_GO/pla/T19_6_3001_4000.R
index 6abad1e..696be87 100644
--- a/code/using_GO/pla/T19_6_3001_4000.R
+++ b/code/using_GO/pla/T19_6_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_6_4001_5000.R b/code/using_GO/pla/T19_6_4001_5000.R
index de6adc4..5592ea6 100644
--- a/code/using_GO/pla/T19_6_4001_5000.R
+++ b/code/using_GO/pla/T19_6_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_6_5001_6000.R b/code/using_GO/pla/T19_6_5001_6000.R
index 9af25ae..8d3f588 100644
--- a/code/using_GO/pla/T19_6_5001_6000.R
+++ b/code/using_GO/pla/T19_6_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_6_6001_7297.R b/code/using_GO/pla/T19_6_6001_7297.R
index 06492fb..c98cce2 100644
--- a/code/using_GO/pla/T19_6_6001_7297.R
+++ b/code/using_GO/pla/T19_6_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_6_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_7_1001_2000.R b/code/using_GO/pla/T19_7_1001_2000.R
index c8d6c10..cf36af3 100644
--- a/code/using_GO/pla/T19_7_1001_2000.R
+++ b/code/using_GO/pla/T19_7_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_7_1_1000.R b/code/using_GO/pla/T19_7_1_1000.R
index 450a7ef..e48d3e7 100644
--- a/code/using_GO/pla/T19_7_1_1000.R
+++ b/code/using_GO/pla/T19_7_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_7_2001_3000.R b/code/using_GO/pla/T19_7_2001_3000.R
index 7cb6b03..4e2b8ed 100644
--- a/code/using_GO/pla/T19_7_2001_3000.R
+++ b/code/using_GO/pla/T19_7_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_7_3001_4000.R b/code/using_GO/pla/T19_7_3001_4000.R
index bffea95..eda96da 100644
--- a/code/using_GO/pla/T19_7_3001_4000.R
+++ b/code/using_GO/pla/T19_7_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_7_4001_5000.R b/code/using_GO/pla/T19_7_4001_5000.R
index f3ff484..1b91da2 100644
--- a/code/using_GO/pla/T19_7_4001_5000.R
+++ b/code/using_GO/pla/T19_7_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_7_5001_6000.R b/code/using_GO/pla/T19_7_5001_6000.R
index 0d79810..d496d98 100644
--- a/code/using_GO/pla/T19_7_5001_6000.R
+++ b/code/using_GO/pla/T19_7_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_7_6001_7297.R b/code/using_GO/pla/T19_7_6001_7297.R
index 9d812e2..dcd1945 100644
--- a/code/using_GO/pla/T19_7_6001_7297.R
+++ b/code/using_GO/pla/T19_7_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_7_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_8_1001_2000.R b/code/using_GO/pla/T19_8_1001_2000.R
index ea6b791..5f5c01e 100644
--- a/code/using_GO/pla/T19_8_1001_2000.R
+++ b/code/using_GO/pla/T19_8_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_8_1_1000.R b/code/using_GO/pla/T19_8_1_1000.R
index e545504..cec93bb 100644
--- a/code/using_GO/pla/T19_8_1_1000.R
+++ b/code/using_GO/pla/T19_8_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_8_2001_3000.R b/code/using_GO/pla/T19_8_2001_3000.R
index d87af76..b3e0edc 100644
--- a/code/using_GO/pla/T19_8_2001_3000.R
+++ b/code/using_GO/pla/T19_8_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_8_3001_4000.R b/code/using_GO/pla/T19_8_3001_4000.R
index 9822cbc..6f8b04d 100644
--- a/code/using_GO/pla/T19_8_3001_4000.R
+++ b/code/using_GO/pla/T19_8_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_8_4001_5000.R b/code/using_GO/pla/T19_8_4001_5000.R
index 4a5b40a..a6a8c95 100644
--- a/code/using_GO/pla/T19_8_4001_5000.R
+++ b/code/using_GO/pla/T19_8_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_8_5001_6000.R b/code/using_GO/pla/T19_8_5001_6000.R
index 766d4f8..6a09d14 100644
--- a/code/using_GO/pla/T19_8_5001_6000.R
+++ b/code/using_GO/pla/T19_8_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T19_8_6001_7297.R b/code/using_GO/pla/T19_8_6001_7297.R
index c699d86..8a3e143 100644
--- a/code/using_GO/pla/T19_8_6001_7297.R
+++ b/code/using_GO/pla/T19_8_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T19_8_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_1_1001_2000.R b/code/using_GO/pla/T20_1_1001_2000.R
index e4f24a8..2027d48 100644
--- a/code/using_GO/pla/T20_1_1001_2000.R
+++ b/code/using_GO/pla/T20_1_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_1_1_1000.R b/code/using_GO/pla/T20_1_1_1000.R
index 7b0d3d3..b683a67 100644
--- a/code/using_GO/pla/T20_1_1_1000.R
+++ b/code/using_GO/pla/T20_1_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_1_2001_3000.R b/code/using_GO/pla/T20_1_2001_3000.R
index dac8bf8..8ab5747 100644
--- a/code/using_GO/pla/T20_1_2001_3000.R
+++ b/code/using_GO/pla/T20_1_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_1_3001_4000.R b/code/using_GO/pla/T20_1_3001_4000.R
index 789b040..c14f8a6 100644
--- a/code/using_GO/pla/T20_1_3001_4000.R
+++ b/code/using_GO/pla/T20_1_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_1_4001_5000.R b/code/using_GO/pla/T20_1_4001_5000.R
index 4a8b356..8863913 100644
--- a/code/using_GO/pla/T20_1_4001_5000.R
+++ b/code/using_GO/pla/T20_1_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_1_5001_6000.R b/code/using_GO/pla/T20_1_5001_6000.R
index ed86247..7228e43 100644
--- a/code/using_GO/pla/T20_1_5001_6000.R
+++ b/code/using_GO/pla/T20_1_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_1_6001_7297.R b/code/using_GO/pla/T20_1_6001_7297.R
index ce3fb32..b7df920 100644
--- a/code/using_GO/pla/T20_1_6001_7297.R
+++ b/code/using_GO/pla/T20_1_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_1_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_2_1001_2000.R b/code/using_GO/pla/T20_2_1001_2000.R
index 7242215..6fe0f91 100644
--- a/code/using_GO/pla/T20_2_1001_2000.R
+++ b/code/using_GO/pla/T20_2_1001_2000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_2_1_1000.R b/code/using_GO/pla/T20_2_1_1000.R
index ada4b08..a376915 100644
--- a/code/using_GO/pla/T20_2_1_1000.R
+++ b/code/using_GO/pla/T20_2_1_1000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_2_2001_3000.R b/code/using_GO/pla/T20_2_2001_3000.R
index 5dbc48d..b472bad 100644
--- a/code/using_GO/pla/T20_2_2001_3000.R
+++ b/code/using_GO/pla/T20_2_2001_3000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_2_3001_4000.R b/code/using_GO/pla/T20_2_3001_4000.R
index 0824607..82f45c0 100644
--- a/code/using_GO/pla/T20_2_3001_4000.R
+++ b/code/using_GO/pla/T20_2_3001_4000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_2_4001_5000.R b/code/using_GO/pla/T20_2_4001_5000.R
index fe263e2..a88e2bc 100644
--- a/code/using_GO/pla/T20_2_4001_5000.R
+++ b/code/using_GO/pla/T20_2_4001_5000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_2_5001_6000.R b/code/using_GO/pla/T20_2_5001_6000.R
index d10b150..d7bedd4 100644
--- a/code/using_GO/pla/T20_2_5001_6000.R
+++ b/code/using_GO/pla/T20_2_5001_6000.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/T20_2_6001_7297.R b/code/using_GO/pla/T20_2_6001_7297.R
index 0b0f475..2b8eac6 100644
--- a/code/using_GO/pla/T20_2_6001_7297.R
+++ b/code/using_GO/pla/T20_2_6001_7297.R
@@ -8,7 +8,25 @@ is.installed <- function(mypkg)
 } 
 ########################################################################################
 
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+
+setwd(paste0(wdir,"/",wd,"/8old"));
+########################################################################################
 
 #if (!is.installed("backports"))
 #{
@@ -32,26 +50,26 @@ library('qgg')
 library('dplyr')
 ###########################################################################################
 message("Loading data...")
-MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds")
-accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds")
-all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds")
-ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds")
-W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata")
-MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata")
-load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata")
-go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds")		#7432
-go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds")	#7432
-go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds")			#7432
-markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds")				#7297	excluding those go terms with zero markers
-setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds")					#7297	excluding those go terms with zero markers
-rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds")					#7297	excluding those go terms with zero markers
-nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds")					#7297	excluding those go terms with zero markers
-nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds")					#7297	excluding those go terms with zero markers
-GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds")						#7297	excluding those go terms with zero markers
-rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds")						#7297	excluding those go terms with zero markers	
+MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds")
+accessions=readRDS(file="../../../../data/accessions.rds")
+all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds")
+ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds")
+W=readRDS(file="../../../../data/W.rds")
+load(file="../../../../data/G.Rdata")
+MAC_df=readRDS(file="../../../../data/MAC_df.rds")
+load(file="../../../../data/Pheno_pla.Rdata")
+load(file="../../../../data/geno_pheno_pla.Rdata")
+load(file="../../../../data/pheno_df_pla.Rdata")
+go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds")		
+go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds")	
+go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds")			
+markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds")				
+setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds")					
+rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds")					
+nsets=readRDS(file="../../../../data/priors/go/nsets.rds")					
+nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds")					
+GF=readRDS(file="../../../../data/priors/go/GF.rds")						
+rGF=readRDS(file="../../../../data/priors/go/rGF.rds")							
 ########################################################################################
 #filter
 n=length(go_all_genes_number[go_all_markers_number>0])
@@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297]
 
 ###########################################################################################
 cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); 
- gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds")
+ gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds")
 n_folds <- 8
 
 T20_2_gblup_variances_all=rep(list(list()),cycles)
diff --git a/code/using_GO/pla/gblup_vs_gfblup_using_go_analysis1.R b/code/using_GO/pla/gblup_vs_gfblup_using_go_analysis1.R
index b950c2c..a96dbba 100644
--- a/code/using_GO/pla/gblup_vs_gfblup_using_go_analysis1.R
+++ b/code/using_GO/pla/gblup_vs_gfblup_using_go_analysis1.R
@@ -2,7 +2,25 @@
 ##################################################################################################################################
 #	A	N	A	L	Y	S	I	S
 ##################################################################################################################################
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+setwd(paste0(wdir,"/",wd,"/8fold/"));
+#################################################################################################################
+
 require(GO.db)
 
 T20_2_gblup_variances_all=readRDS(file="./T20_2_gblup_variances_all.rds")
diff --git a/code/using_GO/psii/8fold/combine.R b/code/using_GO/psii/8fold/combine.R
new file mode 100644
index 0000000..374cd42
--- /dev/null
+++ b/code/using_GO/psii/8fold/combine.R
@@ -0,0 +1,1258 @@
+##################################################################################################################################
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+setwd(paste0(wdir,"/",wd));
+##################################################################################################################################
+L1_1_gblup_prediction_all_1_1000=readRDS(file="L1_1_gblup_prediction_all_1_1000.rds")
+L1_1_gblup_prediction_all_1001_2000=readRDS(file="L1_1_gblup_prediction_all_1001_2000.rds")
+L1_1_gblup_prediction_all_2001_3000=readRDS(file="L1_1_gblup_prediction_all_2001_3000.rds")
+L1_1_gblup_prediction_all_3001_4000=readRDS(file="L1_1_gblup_prediction_all_3001_4000.rds")
+L1_1_gblup_prediction_all_4001_5000=readRDS(file="L1_1_gblup_prediction_all_4001_5000.rds")
+L1_1_gblup_prediction_all_5001_6000=readRDS(file="L1_1_gblup_prediction_all_5001_6000.rds")
+L1_1_gblup_prediction_all_6001_7297=readRDS(file="L1_1_gblup_prediction_all_6001_7297.rds")
+L1_1_gblup_prediction_all=c(L1_1_gblup_prediction_all_1_1000,L1_1_gblup_prediction_all_1001_2000,L1_1_gblup_prediction_all_2001_3000,L1_1_gblup_prediction_all_3001_4000,L1_1_gblup_prediction_all_4001_5000,L1_1_gblup_prediction_all_5001_6000,L1_1_gblup_prediction_all_6001_7297)
+
+L1_1_gblup_variances_all_1_1000=readRDS(file="L1_1_gblup_variances_all_1_1000.rds")
+L1_1_gblup_variances_all_1001_2000=readRDS(file="L1_1_gblup_variances_all_1001_2000.rds")
+L1_1_gblup_variances_all_2001_3000=readRDS(file="L1_1_gblup_variances_all_2001_3000.rds")
+L1_1_gblup_variances_all_3001_4000=readRDS(file="L1_1_gblup_variances_all_3001_4000.rds")
+L1_1_gblup_variances_all_4001_5000=readRDS(file="L1_1_gblup_variances_all_4001_5000.rds")
+L1_1_gblup_variances_all_5001_6000=readRDS(file="L1_1_gblup_variances_all_5001_6000.rds")
+L1_1_gblup_variances_all_6001_7297=readRDS(file="L1_1_gblup_variances_all_6001_7297.rds")
+L1_1_gblup_variances_all=c(L1_1_gblup_variances_all_1_1000,L1_1_gblup_variances_all_1001_2000,L1_1_gblup_variances_all_2001_3000,L1_1_gblup_variances_all_3001_4000,L1_1_gblup_variances_all_4001_5000,L1_1_gblup_variances_all_5001_6000,L1_1_gblup_variances_all_6001_7297)
+
+saveRDS(L1_1_gblup_prediction_all,"L1_1_gblup_prediction_all.rds")
+saveRDS(L1_1_gblup_variances_all,"L1_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L1_1_gfblup_prediction_all_1_1000=readRDS(file="L1_1_gfblup_prediction_all_1_1000.rds")
+L1_1_gfblup_prediction_all_1001_2000=readRDS(file="L1_1_gfblup_prediction_all_1001_2000.rds")
+L1_1_gfblup_prediction_all_2001_3000=readRDS(file="L1_1_gfblup_prediction_all_2001_3000.rds")
+L1_1_gfblup_prediction_all_3001_4000=readRDS(file="L1_1_gfblup_prediction_all_3001_4000.rds")
+L1_1_gfblup_prediction_all_4001_5000=readRDS(file="L1_1_gfblup_prediction_all_4001_5000.rds")
+L1_1_gfblup_prediction_all_5001_6000=readRDS(file="L1_1_gfblup_prediction_all_5001_6000.rds")
+L1_1_gfblup_prediction_all_6001_7297=readRDS(file="L1_1_gfblup_prediction_all_6001_7297.rds")
+
+L1_1_gfblup_variances_all_1_1000=readRDS(file="L1_1_gfblup_variances_all_1_1000.rds")
+L1_1_gfblup_variances_all_1001_2000=readRDS(file="L1_1_gfblup_variances_all_1001_2000.rds")
+L1_1_gfblup_variances_all_2001_3000=readRDS(file="L1_1_gfblup_variances_all_2001_3000.rds")
+L1_1_gfblup_variances_all_3001_4000=readRDS(file="L1_1_gfblup_variances_all_3001_4000.rds")
+L1_1_gfblup_variances_all_4001_5000=readRDS(file="L1_1_gfblup_variances_all_4001_5000.rds")
+L1_1_gfblup_variances_all_5001_6000=readRDS(file="L1_1_gfblup_variances_all_5001_6000.rds")
+L1_1_gfblup_variances_all_6001_7297=readRDS(file="L1_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(L1_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L1_1_gfblup_variances_all=rep(list(list()),cycles)
+L1_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_1_1000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_1001_2000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_2001_3000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_3001_4000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_4001_5000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_5001_6000[[r]])
+	L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_6001_7297[[r]])
+
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_1_1000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_1001_2000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_2001_3000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_3001_4000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_4001_5000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_5001_6000[[r]])
+	L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(L1_1_gfblup_prediction_all,"L1_1_gfblup_prediction_all.rds")
+saveRDS(L1_1_gfblup_variances_all,"L1_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+L1_2_gblup_prediction_all_1_1000=readRDS(file="L1_2_gblup_prediction_all_1_1000.rds")
+L1_2_gblup_prediction_all_1001_2000=readRDS(file="L1_2_gblup_prediction_all_1001_2000.rds")
+L1_2_gblup_prediction_all_2001_3000=readRDS(file="L1_2_gblup_prediction_all_2001_3000.rds")
+L1_2_gblup_prediction_all_3001_4000=readRDS(file="L1_2_gblup_prediction_all_3001_4000.rds")
+L1_2_gblup_prediction_all_4001_5000=readRDS(file="L1_2_gblup_prediction_all_4001_5000.rds")
+L1_2_gblup_prediction_all_5001_6000=readRDS(file="L1_2_gblup_prediction_all_5001_6000.rds")
+L1_2_gblup_prediction_all_6001_7297=readRDS(file="L1_2_gblup_prediction_all_6001_7297.rds")
+L1_2_gblup_prediction_all=c(L1_2_gblup_prediction_all_1_1000,L1_2_gblup_prediction_all_1001_2000,L1_2_gblup_prediction_all_2001_3000,L1_2_gblup_prediction_all_3001_4000,L1_2_gblup_prediction_all_4001_5000,L1_2_gblup_prediction_all_5001_6000,L1_2_gblup_prediction_all_6001_7297)
+
+L1_2_gblup_variances_all_1_1000=readRDS(file="L1_2_gblup_variances_all_1_1000.rds")
+L1_2_gblup_variances_all_1001_2000=readRDS(file="L1_2_gblup_variances_all_1001_2000.rds")
+L1_2_gblup_variances_all_2001_3000=readRDS(file="L1_2_gblup_variances_all_2001_3000.rds")
+L1_2_gblup_variances_all_3001_4000=readRDS(file="L1_2_gblup_variances_all_3001_4000.rds")
+L1_2_gblup_variances_all_4001_5000=readRDS(file="L1_2_gblup_variances_all_4001_5000.rds")
+L1_2_gblup_variances_all_5001_6000=readRDS(file="L1_2_gblup_variances_all_5001_6000.rds")
+L1_2_gblup_variances_all_6001_7297=readRDS(file="L1_2_gblup_variances_all_6001_7297.rds")
+L1_2_gblup_variances_all=c(L1_2_gblup_variances_all_1_1000,L1_2_gblup_variances_all_1001_2000,L1_2_gblup_variances_all_2001_3000,L1_2_gblup_variances_all_3001_4000,L1_2_gblup_variances_all_4001_5000,L1_2_gblup_variances_all_5001_6000,L1_2_gblup_variances_all_6001_7297)
+
+saveRDS(L1_2_gblup_prediction_all,"L1_2_gblup_prediction_all.rds")
+saveRDS(L1_2_gblup_variances_all,"L1_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L1_2_gfblup_prediction_all_1_1000=readRDS(file="L1_2_gfblup_prediction_all_1_1000.rds")
+L1_2_gfblup_prediction_all_1001_2000=readRDS(file="L1_2_gfblup_prediction_all_1001_2000.rds")
+L1_2_gfblup_prediction_all_2001_3000=readRDS(file="L1_2_gfblup_prediction_all_2001_3000.rds")
+L1_2_gfblup_prediction_all_3001_4000=readRDS(file="L1_2_gfblup_prediction_all_3001_4000.rds")
+L1_2_gfblup_prediction_all_4001_5000=readRDS(file="L1_2_gfblup_prediction_all_4001_5000.rds")
+L1_2_gfblup_prediction_all_5001_6000=readRDS(file="L1_2_gfblup_prediction_all_5001_6000.rds")
+L1_2_gfblup_prediction_all_6001_7297=readRDS(file="L1_2_gfblup_prediction_all_6001_7297.rds")
+
+L1_2_gfblup_variances_all_1_1000=readRDS(file="L1_2_gfblup_variances_all_1_1000.rds")
+L1_2_gfblup_variances_all_1001_2000=readRDS(file="L1_2_gfblup_variances_all_1001_2000.rds")
+L1_2_gfblup_variances_all_2001_3000=readRDS(file="L1_2_gfblup_variances_all_2001_3000.rds")
+L1_2_gfblup_variances_all_3001_4000=readRDS(file="L1_2_gfblup_variances_all_3001_4000.rds")
+L1_2_gfblup_variances_all_4001_5000=readRDS(file="L1_2_gfblup_variances_all_4001_5000.rds")
+L1_2_gfblup_variances_all_5001_6000=readRDS(file="L1_2_gfblup_variances_all_5001_6000.rds")
+L1_2_gfblup_variances_all_6001_7297=readRDS(file="L1_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(L1_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L1_2_gfblup_variances_all=rep(list(list()),cycles)
+L1_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_1_1000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_1001_2000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_2001_3000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_3001_4000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_4001_5000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_5001_6000[[r]])
+	L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_6001_7297[[r]])
+
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_1_1000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_1001_2000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_2001_3000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_3001_4000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_4001_5000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_5001_6000[[r]])
+	L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(L1_2_gfblup_prediction_all,"L1_2_gfblup_prediction_all.rds")
+saveRDS(L1_2_gfblup_variances_all,"L1_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+L1_3_gblup_prediction_all_1_1000=readRDS(file="L1_3_gblup_prediction_all_1_1000.rds")
+L1_3_gblup_prediction_all_1001_2000=readRDS(file="L1_3_gblup_prediction_all_1001_2000.rds")
+L1_3_gblup_prediction_all_2001_3000=readRDS(file="L1_3_gblup_prediction_all_2001_3000.rds")
+L1_3_gblup_prediction_all_3001_4000=readRDS(file="L1_3_gblup_prediction_all_3001_4000.rds")
+L1_3_gblup_prediction_all_4001_5000=readRDS(file="L1_3_gblup_prediction_all_4001_5000.rds")
+L1_3_gblup_prediction_all_5001_6000=readRDS(file="L1_3_gblup_prediction_all_5001_6000.rds")
+L1_3_gblup_prediction_all_6001_7297=readRDS(file="L1_3_gblup_prediction_all_6001_7297.rds")
+L1_3_gblup_prediction_all=c(L1_3_gblup_prediction_all_1_1000,L1_3_gblup_prediction_all_1001_2000,L1_3_gblup_prediction_all_2001_3000,L1_3_gblup_prediction_all_3001_4000,L1_3_gblup_prediction_all_4001_5000,L1_3_gblup_prediction_all_5001_6000,L1_3_gblup_prediction_all_6001_7297)
+
+L1_3_gblup_variances_all_1_1000=readRDS(file="L1_3_gblup_variances_all_1_1000.rds")
+L1_3_gblup_variances_all_1001_2000=readRDS(file="L1_3_gblup_variances_all_1001_2000.rds")
+L1_3_gblup_variances_all_2001_3000=readRDS(file="L1_3_gblup_variances_all_2001_3000.rds")
+L1_3_gblup_variances_all_3001_4000=readRDS(file="L1_3_gblup_variances_all_3001_4000.rds")
+L1_3_gblup_variances_all_4001_5000=readRDS(file="L1_3_gblup_variances_all_4001_5000.rds")
+L1_3_gblup_variances_all_5001_6000=readRDS(file="L1_3_gblup_variances_all_5001_6000.rds")
+L1_3_gblup_variances_all_6001_7297=readRDS(file="L1_3_gblup_variances_all_6001_7297.rds")
+L1_3_gblup_variances_all=c(L1_3_gblup_variances_all_1_1000,L1_3_gblup_variances_all_1001_2000,L1_3_gblup_variances_all_2001_3000,L1_3_gblup_variances_all_3001_4000,L1_3_gblup_variances_all_4001_5000,L1_3_gblup_variances_all_5001_6000,L1_3_gblup_variances_all_6001_7297)
+
+saveRDS(L1_3_gblup_prediction_all,"L1_3_gblup_prediction_all.rds")
+saveRDS(L1_3_gblup_variances_all,"L1_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L1_3_gfblup_prediction_all_1_1000=readRDS(file="L1_3_gfblup_prediction_all_1_1000.rds")
+L1_3_gfblup_prediction_all_1001_2000=readRDS(file="L1_3_gfblup_prediction_all_1001_2000.rds")
+L1_3_gfblup_prediction_all_2001_3000=readRDS(file="L1_3_gfblup_prediction_all_2001_3000.rds")
+L1_3_gfblup_prediction_all_3001_4000=readRDS(file="L1_3_gfblup_prediction_all_3001_4000.rds")
+L1_3_gfblup_prediction_all_4001_5000=readRDS(file="L1_3_gfblup_prediction_all_4001_5000.rds")
+L1_3_gfblup_prediction_all_5001_6000=readRDS(file="L1_3_gfblup_prediction_all_5001_6000.rds")
+L1_3_gfblup_prediction_all_6001_7297=readRDS(file="L1_3_gfblup_prediction_all_6001_7297.rds")
+
+L1_3_gfblup_variances_all_1_1000=readRDS(file="L1_3_gfblup_variances_all_1_1000.rds")
+L1_3_gfblup_variances_all_1001_2000=readRDS(file="L1_3_gfblup_variances_all_1001_2000.rds")
+L1_3_gfblup_variances_all_2001_3000=readRDS(file="L1_3_gfblup_variances_all_2001_3000.rds")
+L1_3_gfblup_variances_all_3001_4000=readRDS(file="L1_3_gfblup_variances_all_3001_4000.rds")
+L1_3_gfblup_variances_all_4001_5000=readRDS(file="L1_3_gfblup_variances_all_4001_5000.rds")
+L1_3_gfblup_variances_all_5001_6000=readRDS(file="L1_3_gfblup_variances_all_5001_6000.rds")
+L1_3_gfblup_variances_all_6001_7297=readRDS(file="L1_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(L1_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L1_3_gfblup_variances_all=rep(list(list()),cycles)
+L1_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_1_1000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_1001_2000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_2001_3000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_3001_4000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_4001_5000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_5001_6000[[r]])
+	L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_6001_7297[[r]])
+
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_1_1000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_1001_2000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_2001_3000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_3001_4000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_4001_5000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_5001_6000[[r]])
+	L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(L1_3_gfblup_prediction_all,"L1_3_gfblup_prediction_all.rds")
+saveRDS(L1_3_gfblup_variances_all,"L1_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+L2_1_gblup_prediction_all_1_1000=readRDS(file="L2_1_gblup_prediction_all_1_1000.rds")
+L2_1_gblup_prediction_all_1001_2000=readRDS(file="L2_1_gblup_prediction_all_1001_2000.rds")
+L2_1_gblup_prediction_all_2001_3000=readRDS(file="L2_1_gblup_prediction_all_2001_3000.rds")
+L2_1_gblup_prediction_all_3001_4000=readRDS(file="L2_1_gblup_prediction_all_3001_4000.rds")
+L2_1_gblup_prediction_all_4001_5000=readRDS(file="L2_1_gblup_prediction_all_4001_5000.rds")
+L2_1_gblup_prediction_all_5001_6000=readRDS(file="L2_1_gblup_prediction_all_5001_6000.rds")
+L2_1_gblup_prediction_all_6001_7297=readRDS(file="L2_1_gblup_prediction_all_6001_7297.rds")
+L2_1_gblup_prediction_all=c(L2_1_gblup_prediction_all_1_1000,L2_1_gblup_prediction_all_1001_2000,L2_1_gblup_prediction_all_2001_3000,L2_1_gblup_prediction_all_3001_4000,L2_1_gblup_prediction_all_4001_5000,L2_1_gblup_prediction_all_5001_6000,L2_1_gblup_prediction_all_6001_7297)
+
+L2_1_gblup_variances_all_1_1000=readRDS(file="L2_1_gblup_variances_all_1_1000.rds")
+L2_1_gblup_variances_all_1001_2000=readRDS(file="L2_1_gblup_variances_all_1001_2000.rds")
+L2_1_gblup_variances_all_2001_3000=readRDS(file="L2_1_gblup_variances_all_2001_3000.rds")
+L2_1_gblup_variances_all_3001_4000=readRDS(file="L2_1_gblup_variances_all_3001_4000.rds")
+L2_1_gblup_variances_all_4001_5000=readRDS(file="L2_1_gblup_variances_all_4001_5000.rds")
+L2_1_gblup_variances_all_5001_6000=readRDS(file="L2_1_gblup_variances_all_5001_6000.rds")
+L2_1_gblup_variances_all_6001_7297=readRDS(file="L2_1_gblup_variances_all_6001_7297.rds")
+L2_1_gblup_variances_all=c(L2_1_gblup_variances_all_1_1000,L2_1_gblup_variances_all_1001_2000,L2_1_gblup_variances_all_2001_3000,L2_1_gblup_variances_all_3001_4000,L2_1_gblup_variances_all_4001_5000,L2_1_gblup_variances_all_5001_6000,L2_1_gblup_variances_all_6001_7297)
+
+saveRDS(L2_1_gblup_prediction_all,"L2_1_gblup_prediction_all.rds")
+saveRDS(L2_1_gblup_variances_all,"L2_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L2_1_gfblup_prediction_all_1_1000=readRDS(file="L2_1_gfblup_prediction_all_1_1000.rds")
+L2_1_gfblup_prediction_all_1001_2000=readRDS(file="L2_1_gfblup_prediction_all_1001_2000.rds")
+L2_1_gfblup_prediction_all_2001_3000=readRDS(file="L2_1_gfblup_prediction_all_2001_3000.rds")
+L2_1_gfblup_prediction_all_3001_4000=readRDS(file="L2_1_gfblup_prediction_all_3001_4000.rds")
+L2_1_gfblup_prediction_all_4001_5000=readRDS(file="L2_1_gfblup_prediction_all_4001_5000.rds")
+L2_1_gfblup_prediction_all_5001_6000=readRDS(file="L2_1_gfblup_prediction_all_5001_6000.rds")
+L2_1_gfblup_prediction_all_6001_7297=readRDS(file="L2_1_gfblup_prediction_all_6001_7297.rds")
+
+L2_1_gfblup_variances_all_1_1000=readRDS(file="L2_1_gfblup_variances_all_1_1000.rds")
+L2_1_gfblup_variances_all_1001_2000=readRDS(file="L2_1_gfblup_variances_all_1001_2000.rds")
+L2_1_gfblup_variances_all_2001_3000=readRDS(file="L2_1_gfblup_variances_all_2001_3000.rds")
+L2_1_gfblup_variances_all_3001_4000=readRDS(file="L2_1_gfblup_variances_all_3001_4000.rds")
+L2_1_gfblup_variances_all_4001_5000=readRDS(file="L2_1_gfblup_variances_all_4001_5000.rds")
+L2_1_gfblup_variances_all_5001_6000=readRDS(file="L2_1_gfblup_variances_all_5001_6000.rds")
+L2_1_gfblup_variances_all_6001_7297=readRDS(file="L2_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(L2_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L2_1_gfblup_variances_all=rep(list(list()),cycles)
+L2_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_1_1000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_1001_2000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_2001_3000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_3001_4000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_4001_5000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_5001_6000[[r]])
+	L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_6001_7297[[r]])
+
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_1_1000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_1001_2000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_2001_3000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_3001_4000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_4001_5000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_5001_6000[[r]])
+	L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(L2_1_gfblup_prediction_all,"L2_1_gfblup_prediction_all.rds")
+saveRDS(L2_1_gfblup_variances_all,"L2_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+L2_2_gblup_prediction_all_1_1000=readRDS(file="L2_2_gblup_prediction_all_1_1000.rds")
+L2_2_gblup_prediction_all_1001_2000=readRDS(file="L2_2_gblup_prediction_all_1001_2000.rds")
+L2_2_gblup_prediction_all_2001_3000=readRDS(file="L2_2_gblup_prediction_all_2001_3000.rds")
+L2_2_gblup_prediction_all_3001_4000=readRDS(file="L2_2_gblup_prediction_all_3001_4000.rds")
+L2_2_gblup_prediction_all_4001_5000=readRDS(file="L2_2_gblup_prediction_all_4001_5000.rds")
+L2_2_gblup_prediction_all_5001_6000=readRDS(file="L2_2_gblup_prediction_all_5001_6000.rds")
+L2_2_gblup_prediction_all_6001_7297=readRDS(file="L2_2_gblup_prediction_all_6001_7297.rds")
+L2_2_gblup_prediction_all=c(L2_2_gblup_prediction_all_1_1000,L2_2_gblup_prediction_all_1001_2000,L2_2_gblup_prediction_all_2001_3000,L2_2_gblup_prediction_all_3001_4000,L2_2_gblup_prediction_all_4001_5000,L2_2_gblup_prediction_all_5001_6000,L2_2_gblup_prediction_all_6001_7297)
+
+L2_2_gblup_variances_all_1_1000=readRDS(file="L2_2_gblup_variances_all_1_1000.rds")
+L2_2_gblup_variances_all_1001_2000=readRDS(file="L2_2_gblup_variances_all_1001_2000.rds")
+L2_2_gblup_variances_all_2001_3000=readRDS(file="L2_2_gblup_variances_all_2001_3000.rds")
+L2_2_gblup_variances_all_3001_4000=readRDS(file="L2_2_gblup_variances_all_3001_4000.rds")
+L2_2_gblup_variances_all_4001_5000=readRDS(file="L2_2_gblup_variances_all_4001_5000.rds")
+L2_2_gblup_variances_all_5001_6000=readRDS(file="L2_2_gblup_variances_all_5001_6000.rds")
+L2_2_gblup_variances_all_6001_7297=readRDS(file="L2_2_gblup_variances_all_6001_7297.rds")
+L2_2_gblup_variances_all=c(L2_2_gblup_variances_all_1_1000,L2_2_gblup_variances_all_1001_2000,L2_2_gblup_variances_all_2001_3000,L2_2_gblup_variances_all_3001_4000,L2_2_gblup_variances_all_4001_5000,L2_2_gblup_variances_all_5001_6000,L2_2_gblup_variances_all_6001_7297)
+
+saveRDS(L2_2_gblup_prediction_all,"L2_2_gblup_prediction_all.rds")
+saveRDS(L2_2_gblup_variances_all,"L2_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L2_2_gfblup_prediction_all_1_1000=readRDS(file="L2_2_gfblup_prediction_all_1_1000.rds")
+L2_2_gfblup_prediction_all_1001_2000=readRDS(file="L2_2_gfblup_prediction_all_1001_2000.rds")
+L2_2_gfblup_prediction_all_2001_3000=readRDS(file="L2_2_gfblup_prediction_all_2001_3000.rds")
+L2_2_gfblup_prediction_all_3001_4000=readRDS(file="L2_2_gfblup_prediction_all_3001_4000.rds")
+L2_2_gfblup_prediction_all_4001_5000=readRDS(file="L2_2_gfblup_prediction_all_4001_5000.rds")
+L2_2_gfblup_prediction_all_5001_6000=readRDS(file="L2_2_gfblup_prediction_all_5001_6000.rds")
+L2_2_gfblup_prediction_all_6001_7297=readRDS(file="L2_2_gfblup_prediction_all_6001_7297.rds")
+
+L2_2_gfblup_variances_all_1_1000=readRDS(file="L2_2_gfblup_variances_all_1_1000.rds")
+L2_2_gfblup_variances_all_1001_2000=readRDS(file="L2_2_gfblup_variances_all_1001_2000.rds")
+L2_2_gfblup_variances_all_2001_3000=readRDS(file="L2_2_gfblup_variances_all_2001_3000.rds")
+L2_2_gfblup_variances_all_3001_4000=readRDS(file="L2_2_gfblup_variances_all_3001_4000.rds")
+L2_2_gfblup_variances_all_4001_5000=readRDS(file="L2_2_gfblup_variances_all_4001_5000.rds")
+L2_2_gfblup_variances_all_5001_6000=readRDS(file="L2_2_gfblup_variances_all_5001_6000.rds")
+L2_2_gfblup_variances_all_6001_7297=readRDS(file="L2_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(L2_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L2_2_gfblup_variances_all=rep(list(list()),cycles)
+L2_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_1_1000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_1001_2000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_2001_3000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_3001_4000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_4001_5000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_5001_6000[[r]])
+	L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_6001_7297[[r]])
+
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_1_1000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_1001_2000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_2001_3000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_3001_4000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_4001_5000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_5001_6000[[r]])
+	L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(L2_2_gfblup_prediction_all,"L2_2_gfblup_prediction_all.rds")
+saveRDS(L2_2_gfblup_variances_all,"L2_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+L2_3_gblup_prediction_all_1_1000=readRDS(file="L2_3_gblup_prediction_all_1_1000.rds")
+L2_3_gblup_prediction_all_1001_2000=readRDS(file="L2_3_gblup_prediction_all_1001_2000.rds")
+L2_3_gblup_prediction_all_2001_3000=readRDS(file="L2_3_gblup_prediction_all_2001_3000.rds")
+L2_3_gblup_prediction_all_3001_4000=readRDS(file="L2_3_gblup_prediction_all_3001_4000.rds")
+L2_3_gblup_prediction_all_4001_5000=readRDS(file="L2_3_gblup_prediction_all_4001_5000.rds")
+L2_3_gblup_prediction_all_5001_6000=readRDS(file="L2_3_gblup_prediction_all_5001_6000.rds")
+L2_3_gblup_prediction_all_6001_7297=readRDS(file="L2_3_gblup_prediction_all_6001_7297.rds")
+L2_3_gblup_prediction_all=c(L2_3_gblup_prediction_all_1_1000,L2_3_gblup_prediction_all_1001_2000,L2_3_gblup_prediction_all_2001_3000,L2_3_gblup_prediction_all_3001_4000,L2_3_gblup_prediction_all_4001_5000,L2_3_gblup_prediction_all_5001_6000,L2_3_gblup_prediction_all_6001_7297)
+
+L2_3_gblup_variances_all_1_1000=readRDS(file="L2_3_gblup_variances_all_1_1000.rds")
+L2_3_gblup_variances_all_1001_2000=readRDS(file="L2_3_gblup_variances_all_1001_2000.rds")
+L2_3_gblup_variances_all_2001_3000=readRDS(file="L2_3_gblup_variances_all_2001_3000.rds")
+L2_3_gblup_variances_all_3001_4000=readRDS(file="L2_3_gblup_variances_all_3001_4000.rds")
+L2_3_gblup_variances_all_4001_5000=readRDS(file="L2_3_gblup_variances_all_4001_5000.rds")
+L2_3_gblup_variances_all_5001_6000=readRDS(file="L2_3_gblup_variances_all_5001_6000.rds")
+L2_3_gblup_variances_all_6001_7297=readRDS(file="L2_3_gblup_variances_all_6001_7297.rds")
+L2_3_gblup_variances_all=c(L2_3_gblup_variances_all_1_1000,L2_3_gblup_variances_all_1001_2000,L2_3_gblup_variances_all_2001_3000,L2_3_gblup_variances_all_3001_4000,L2_3_gblup_variances_all_4001_5000,L2_3_gblup_variances_all_5001_6000,L2_3_gblup_variances_all_6001_7297)
+
+saveRDS(L2_3_gblup_prediction_all,"L2_3_gblup_prediction_all.rds")
+saveRDS(L2_3_gblup_variances_all,"L2_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+L2_3_gfblup_prediction_all_1_1000=readRDS(file="L2_3_gfblup_prediction_all_1_1000.rds")
+L2_3_gfblup_prediction_all_1001_2000=readRDS(file="L2_3_gfblup_prediction_all_1001_2000.rds")
+L2_3_gfblup_prediction_all_2001_3000=readRDS(file="L2_3_gfblup_prediction_all_2001_3000.rds")
+L2_3_gfblup_prediction_all_3001_4000=readRDS(file="L2_3_gfblup_prediction_all_3001_4000.rds")
+L2_3_gfblup_prediction_all_4001_5000=readRDS(file="L2_3_gfblup_prediction_all_4001_5000.rds")
+L2_3_gfblup_prediction_all_5001_6000=readRDS(file="L2_3_gfblup_prediction_all_5001_6000.rds")
+L2_3_gfblup_prediction_all_6001_7297=readRDS(file="L2_3_gfblup_prediction_all_6001_7297.rds")
+
+L2_3_gfblup_variances_all_1_1000=readRDS(file="L2_3_gfblup_variances_all_1_1000.rds")
+L2_3_gfblup_variances_all_1001_2000=readRDS(file="L2_3_gfblup_variances_all_1001_2000.rds")
+L2_3_gfblup_variances_all_2001_3000=readRDS(file="L2_3_gfblup_variances_all_2001_3000.rds")
+L2_3_gfblup_variances_all_3001_4000=readRDS(file="L2_3_gfblup_variances_all_3001_4000.rds")
+L2_3_gfblup_variances_all_4001_5000=readRDS(file="L2_3_gfblup_variances_all_4001_5000.rds")
+L2_3_gfblup_variances_all_5001_6000=readRDS(file="L2_3_gfblup_variances_all_5001_6000.rds")
+L2_3_gfblup_variances_all_6001_7297=readRDS(file="L2_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(L2_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+L2_3_gfblup_variances_all=rep(list(list()),cycles)
+L2_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_1_1000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_1001_2000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_2001_3000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_3001_4000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_4001_5000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_5001_6000[[r]])
+	L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_6001_7297[[r]])
+
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_1_1000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_1001_2000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_2001_3000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_3001_4000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_4001_5000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_5001_6000[[r]])
+	L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(L2_3_gfblup_prediction_all,"L2_3_gfblup_prediction_all.rds")
+saveRDS(L2_3_gfblup_variances_all,"L2_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H1_1_gblup_prediction_all_1_1000=readRDS(file="H1_1_gblup_prediction_all_1_1000.rds")
+H1_1_gblup_prediction_all_1001_2000=readRDS(file="H1_1_gblup_prediction_all_1001_2000.rds")
+H1_1_gblup_prediction_all_2001_3000=readRDS(file="H1_1_gblup_prediction_all_2001_3000.rds")
+H1_1_gblup_prediction_all_3001_4000=readRDS(file="H1_1_gblup_prediction_all_3001_4000.rds")
+H1_1_gblup_prediction_all_4001_5000=readRDS(file="H1_1_gblup_prediction_all_4001_5000.rds")
+H1_1_gblup_prediction_all_5001_6000=readRDS(file="H1_1_gblup_prediction_all_5001_6000.rds")
+H1_1_gblup_prediction_all_6001_7297=readRDS(file="H1_1_gblup_prediction_all_6001_7297.rds")
+H1_1_gblup_prediction_all=c(H1_1_gblup_prediction_all_1_1000,H1_1_gblup_prediction_all_1001_2000,H1_1_gblup_prediction_all_2001_3000,H1_1_gblup_prediction_all_3001_4000,H1_1_gblup_prediction_all_4001_5000,H1_1_gblup_prediction_all_5001_6000,H1_1_gblup_prediction_all_6001_7297)
+
+H1_1_gblup_variances_all_1_1000=readRDS(file="H1_1_gblup_variances_all_1_1000.rds")
+H1_1_gblup_variances_all_1001_2000=readRDS(file="H1_1_gblup_variances_all_1001_2000.rds")
+H1_1_gblup_variances_all_2001_3000=readRDS(file="H1_1_gblup_variances_all_2001_3000.rds")
+H1_1_gblup_variances_all_3001_4000=readRDS(file="H1_1_gblup_variances_all_3001_4000.rds")
+H1_1_gblup_variances_all_4001_5000=readRDS(file="H1_1_gblup_variances_all_4001_5000.rds")
+H1_1_gblup_variances_all_5001_6000=readRDS(file="H1_1_gblup_variances_all_5001_6000.rds")
+H1_1_gblup_variances_all_6001_7297=readRDS(file="H1_1_gblup_variances_all_6001_7297.rds")
+H1_1_gblup_variances_all=c(H1_1_gblup_variances_all_1_1000,H1_1_gblup_variances_all_1001_2000,H1_1_gblup_variances_all_2001_3000,H1_1_gblup_variances_all_3001_4000,H1_1_gblup_variances_all_4001_5000,H1_1_gblup_variances_all_5001_6000,H1_1_gblup_variances_all_6001_7297)
+
+saveRDS(H1_1_gblup_prediction_all,"H1_1_gblup_prediction_all.rds")
+saveRDS(H1_1_gblup_variances_all,"H1_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H1_1_gfblup_prediction_all_1_1000=readRDS(file="H1_1_gfblup_prediction_all_1_1000.rds")
+H1_1_gfblup_prediction_all_1001_2000=readRDS(file="H1_1_gfblup_prediction_all_1001_2000.rds")
+H1_1_gfblup_prediction_all_2001_3000=readRDS(file="H1_1_gfblup_prediction_all_2001_3000.rds")
+H1_1_gfblup_prediction_all_3001_4000=readRDS(file="H1_1_gfblup_prediction_all_3001_4000.rds")
+H1_1_gfblup_prediction_all_4001_5000=readRDS(file="H1_1_gfblup_prediction_all_4001_5000.rds")
+H1_1_gfblup_prediction_all_5001_6000=readRDS(file="H1_1_gfblup_prediction_all_5001_6000.rds")
+H1_1_gfblup_prediction_all_6001_7297=readRDS(file="H1_1_gfblup_prediction_all_6001_7297.rds")
+
+H1_1_gfblup_variances_all_1_1000=readRDS(file="H1_1_gfblup_variances_all_1_1000.rds")
+H1_1_gfblup_variances_all_1001_2000=readRDS(file="H1_1_gfblup_variances_all_1001_2000.rds")
+H1_1_gfblup_variances_all_2001_3000=readRDS(file="H1_1_gfblup_variances_all_2001_3000.rds")
+H1_1_gfblup_variances_all_3001_4000=readRDS(file="H1_1_gfblup_variances_all_3001_4000.rds")
+H1_1_gfblup_variances_all_4001_5000=readRDS(file="H1_1_gfblup_variances_all_4001_5000.rds")
+H1_1_gfblup_variances_all_5001_6000=readRDS(file="H1_1_gfblup_variances_all_5001_6000.rds")
+H1_1_gfblup_variances_all_6001_7297=readRDS(file="H1_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H1_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H1_1_gfblup_variances_all=rep(list(list()),cycles)
+H1_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_1_1000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_1001_2000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_2001_3000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_3001_4000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_4001_5000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_5001_6000[[r]])
+	H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_6001_7297[[r]])
+
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_1_1000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_1001_2000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_2001_3000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_3001_4000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_4001_5000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_5001_6000[[r]])
+	H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H1_1_gfblup_prediction_all,"H1_1_gfblup_prediction_all.rds")
+saveRDS(H1_1_gfblup_variances_all,"H1_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+H1_2_gblup_prediction_all_1_1000=readRDS(file="H1_2_gblup_prediction_all_1_1000.rds")
+H1_2_gblup_prediction_all_1001_2000=readRDS(file="H1_2_gblup_prediction_all_1001_2000.rds")
+H1_2_gblup_prediction_all_2001_3000=readRDS(file="H1_2_gblup_prediction_all_2001_3000.rds")
+H1_2_gblup_prediction_all_3001_4000=readRDS(file="H1_2_gblup_prediction_all_3001_4000.rds")
+H1_2_gblup_prediction_all_4001_5000=readRDS(file="H1_2_gblup_prediction_all_4001_5000.rds")
+H1_2_gblup_prediction_all_5001_6000=readRDS(file="H1_2_gblup_prediction_all_5001_6000.rds")
+H1_2_gblup_prediction_all_6001_7297=readRDS(file="H1_2_gblup_prediction_all_6001_7297.rds")
+H1_2_gblup_prediction_all=c(H1_2_gblup_prediction_all_1_1000,H1_2_gblup_prediction_all_1001_2000,H1_2_gblup_prediction_all_2001_3000,H1_2_gblup_prediction_all_3001_4000,H1_2_gblup_prediction_all_4001_5000,H1_2_gblup_prediction_all_5001_6000,H1_2_gblup_prediction_all_6001_7297)
+
+H1_2_gblup_variances_all_1_1000=readRDS(file="H1_2_gblup_variances_all_1_1000.rds")
+H1_2_gblup_variances_all_1001_2000=readRDS(file="H1_2_gblup_variances_all_1001_2000.rds")
+H1_2_gblup_variances_all_2001_3000=readRDS(file="H1_2_gblup_variances_all_2001_3000.rds")
+H1_2_gblup_variances_all_3001_4000=readRDS(file="H1_2_gblup_variances_all_3001_4000.rds")
+H1_2_gblup_variances_all_4001_5000=readRDS(file="H1_2_gblup_variances_all_4001_5000.rds")
+H1_2_gblup_variances_all_5001_6000=readRDS(file="H1_2_gblup_variances_all_5001_6000.rds")
+H1_2_gblup_variances_all_6001_7297=readRDS(file="H1_2_gblup_variances_all_6001_7297.rds")
+H1_2_gblup_variances_all=c(H1_2_gblup_variances_all_1_1000,H1_2_gblup_variances_all_1001_2000,H1_2_gblup_variances_all_2001_3000,H1_2_gblup_variances_all_3001_4000,H1_2_gblup_variances_all_4001_5000,H1_2_gblup_variances_all_5001_6000,H1_2_gblup_variances_all_6001_7297)
+
+saveRDS(H1_2_gblup_prediction_all,"H1_2_gblup_prediction_all.rds")
+saveRDS(H1_2_gblup_variances_all,"H1_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H1_2_gfblup_prediction_all_1_1000=readRDS(file="H1_2_gfblup_prediction_all_1_1000.rds")
+H1_2_gfblup_prediction_all_1001_2000=readRDS(file="H1_2_gfblup_prediction_all_1001_2000.rds")
+H1_2_gfblup_prediction_all_2001_3000=readRDS(file="H1_2_gfblup_prediction_all_2001_3000.rds")
+H1_2_gfblup_prediction_all_3001_4000=readRDS(file="H1_2_gfblup_prediction_all_3001_4000.rds")
+H1_2_gfblup_prediction_all_4001_5000=readRDS(file="H1_2_gfblup_prediction_all_4001_5000.rds")
+H1_2_gfblup_prediction_all_5001_6000=readRDS(file="H1_2_gfblup_prediction_all_5001_6000.rds")
+H1_2_gfblup_prediction_all_6001_7297=readRDS(file="H1_2_gfblup_prediction_all_6001_7297.rds")
+
+H1_2_gfblup_variances_all_1_1000=readRDS(file="H1_2_gfblup_variances_all_1_1000.rds")
+H1_2_gfblup_variances_all_1001_2000=readRDS(file="H1_2_gfblup_variances_all_1001_2000.rds")
+H1_2_gfblup_variances_all_2001_3000=readRDS(file="H1_2_gfblup_variances_all_2001_3000.rds")
+H1_2_gfblup_variances_all_3001_4000=readRDS(file="H1_2_gfblup_variances_all_3001_4000.rds")
+H1_2_gfblup_variances_all_4001_5000=readRDS(file="H1_2_gfblup_variances_all_4001_5000.rds")
+H1_2_gfblup_variances_all_5001_6000=readRDS(file="H1_2_gfblup_variances_all_5001_6000.rds")
+H1_2_gfblup_variances_all_6001_7297=readRDS(file="H1_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H1_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H1_2_gfblup_variances_all=rep(list(list()),cycles)
+H1_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_1_1000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_1001_2000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_2001_3000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_3001_4000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_4001_5000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_5001_6000[[r]])
+	H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_6001_7297[[r]])
+
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_1_1000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_1001_2000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_2001_3000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_3001_4000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_4001_5000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_5001_6000[[r]])
+	H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H1_2_gfblup_prediction_all,"H1_2_gfblup_prediction_all.rds")
+saveRDS(H1_2_gfblup_variances_all,"H1_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+H1_3_gblup_prediction_all_1_1000=readRDS(file="H1_3_gblup_prediction_all_1_1000.rds")
+H1_3_gblup_prediction_all_1001_2000=readRDS(file="H1_3_gblup_prediction_all_1001_2000.rds")
+H1_3_gblup_prediction_all_2001_3000=readRDS(file="H1_3_gblup_prediction_all_2001_3000.rds")
+H1_3_gblup_prediction_all_3001_4000=readRDS(file="H1_3_gblup_prediction_all_3001_4000.rds")
+H1_3_gblup_prediction_all_4001_5000=readRDS(file="H1_3_gblup_prediction_all_4001_5000.rds")
+H1_3_gblup_prediction_all_5001_6000=readRDS(file="H1_3_gblup_prediction_all_5001_6000.rds")
+H1_3_gblup_prediction_all_6001_7297=readRDS(file="H1_3_gblup_prediction_all_6001_7297.rds")
+H1_3_gblup_prediction_all=c(H1_3_gblup_prediction_all_1_1000,H1_3_gblup_prediction_all_1001_2000,H1_3_gblup_prediction_all_2001_3000,H1_3_gblup_prediction_all_3001_4000,H1_3_gblup_prediction_all_4001_5000,H1_3_gblup_prediction_all_5001_6000,H1_3_gblup_prediction_all_6001_7297)
+
+H1_3_gblup_variances_all_1_1000=readRDS(file="H1_3_gblup_variances_all_1_1000.rds")
+H1_3_gblup_variances_all_1001_2000=readRDS(file="H1_3_gblup_variances_all_1001_2000.rds")
+H1_3_gblup_variances_all_2001_3000=readRDS(file="H1_3_gblup_variances_all_2001_3000.rds")
+H1_3_gblup_variances_all_3001_4000=readRDS(file="H1_3_gblup_variances_all_3001_4000.rds")
+H1_3_gblup_variances_all_4001_5000=readRDS(file="H1_3_gblup_variances_all_4001_5000.rds")
+H1_3_gblup_variances_all_5001_6000=readRDS(file="H1_3_gblup_variances_all_5001_6000.rds")
+H1_3_gblup_variances_all_6001_7297=readRDS(file="H1_3_gblup_variances_all_6001_7297.rds")
+H1_3_gblup_variances_all=c(H1_3_gblup_variances_all_1_1000,H1_3_gblup_variances_all_1001_2000,H1_3_gblup_variances_all_2001_3000,H1_3_gblup_variances_all_3001_4000,H1_3_gblup_variances_all_4001_5000,H1_3_gblup_variances_all_5001_6000,H1_3_gblup_variances_all_6001_7297)
+
+saveRDS(H1_3_gblup_prediction_all,"H1_3_gblup_prediction_all.rds")
+saveRDS(H1_3_gblup_variances_all,"H1_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H1_3_gfblup_prediction_all_1_1000=readRDS(file="H1_3_gfblup_prediction_all_1_1000.rds")
+H1_3_gfblup_prediction_all_1001_2000=readRDS(file="H1_3_gfblup_prediction_all_1001_2000.rds")
+H1_3_gfblup_prediction_all_2001_3000=readRDS(file="H1_3_gfblup_prediction_all_2001_3000.rds")
+H1_3_gfblup_prediction_all_3001_4000=readRDS(file="H1_3_gfblup_prediction_all_3001_4000.rds")
+H1_3_gfblup_prediction_all_4001_5000=readRDS(file="H1_3_gfblup_prediction_all_4001_5000.rds")
+H1_3_gfblup_prediction_all_5001_6000=readRDS(file="H1_3_gfblup_prediction_all_5001_6000.rds")
+H1_3_gfblup_prediction_all_6001_7297=readRDS(file="H1_3_gfblup_prediction_all_6001_7297.rds")
+
+H1_3_gfblup_variances_all_1_1000=readRDS(file="H1_3_gfblup_variances_all_1_1000.rds")
+H1_3_gfblup_variances_all_1001_2000=readRDS(file="H1_3_gfblup_variances_all_1001_2000.rds")
+H1_3_gfblup_variances_all_2001_3000=readRDS(file="H1_3_gfblup_variances_all_2001_3000.rds")
+H1_3_gfblup_variances_all_3001_4000=readRDS(file="H1_3_gfblup_variances_all_3001_4000.rds")
+H1_3_gfblup_variances_all_4001_5000=readRDS(file="H1_3_gfblup_variances_all_4001_5000.rds")
+H1_3_gfblup_variances_all_5001_6000=readRDS(file="H1_3_gfblup_variances_all_5001_6000.rds")
+H1_3_gfblup_variances_all_6001_7297=readRDS(file="H1_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H1_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H1_3_gfblup_variances_all=rep(list(list()),cycles)
+H1_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_1_1000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_1001_2000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_2001_3000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_3001_4000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_4001_5000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_5001_6000[[r]])
+	H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_6001_7297[[r]])
+
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_1_1000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_1001_2000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_2001_3000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_3001_4000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_4001_5000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_5001_6000[[r]])
+	H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H1_3_gfblup_prediction_all,"H1_3_gfblup_prediction_all.rds")
+saveRDS(H1_3_gfblup_variances_all,"H1_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+H2_1_gblup_prediction_all_1_1000=readRDS(file="H2_1_gblup_prediction_all_1_1000.rds")
+H2_1_gblup_prediction_all_1001_2000=readRDS(file="H2_1_gblup_prediction_all_1001_2000.rds")
+H2_1_gblup_prediction_all_2001_3000=readRDS(file="H2_1_gblup_prediction_all_2001_3000.rds")
+H2_1_gblup_prediction_all_3001_4000=readRDS(file="H2_1_gblup_prediction_all_3001_4000.rds")
+H2_1_gblup_prediction_all_4001_5000=readRDS(file="H2_1_gblup_prediction_all_4001_5000.rds")
+H2_1_gblup_prediction_all_5001_6000=readRDS(file="H2_1_gblup_prediction_all_5001_6000.rds")
+H2_1_gblup_prediction_all_6001_7297=readRDS(file="H2_1_gblup_prediction_all_6001_7297.rds")
+H2_1_gblup_prediction_all=c(H2_1_gblup_prediction_all_1_1000,H2_1_gblup_prediction_all_1001_2000,H2_1_gblup_prediction_all_2001_3000,H2_1_gblup_prediction_all_3001_4000,H2_1_gblup_prediction_all_4001_5000,H2_1_gblup_prediction_all_5001_6000,H2_1_gblup_prediction_all_6001_7297)
+
+H2_1_gblup_variances_all_1_1000=readRDS(file="H2_1_gblup_variances_all_1_1000.rds")
+H2_1_gblup_variances_all_1001_2000=readRDS(file="H2_1_gblup_variances_all_1001_2000.rds")
+H2_1_gblup_variances_all_2001_3000=readRDS(file="H2_1_gblup_variances_all_2001_3000.rds")
+H2_1_gblup_variances_all_3001_4000=readRDS(file="H2_1_gblup_variances_all_3001_4000.rds")
+H2_1_gblup_variances_all_4001_5000=readRDS(file="H2_1_gblup_variances_all_4001_5000.rds")
+H2_1_gblup_variances_all_5001_6000=readRDS(file="H2_1_gblup_variances_all_5001_6000.rds")
+H2_1_gblup_variances_all_6001_7297=readRDS(file="H2_1_gblup_variances_all_6001_7297.rds")
+H2_1_gblup_variances_all=c(H2_1_gblup_variances_all_1_1000,H2_1_gblup_variances_all_1001_2000,H2_1_gblup_variances_all_2001_3000,H2_1_gblup_variances_all_3001_4000,H2_1_gblup_variances_all_4001_5000,H2_1_gblup_variances_all_5001_6000,H2_1_gblup_variances_all_6001_7297)
+
+saveRDS(H2_1_gblup_prediction_all,"H2_1_gblup_prediction_all.rds")
+saveRDS(H2_1_gblup_variances_all,"H2_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H2_1_gfblup_prediction_all_1_1000=readRDS(file="H2_1_gfblup_prediction_all_1_1000.rds")
+H2_1_gfblup_prediction_all_1001_2000=readRDS(file="H2_1_gfblup_prediction_all_1001_2000.rds")
+H2_1_gfblup_prediction_all_2001_3000=readRDS(file="H2_1_gfblup_prediction_all_2001_3000.rds")
+H2_1_gfblup_prediction_all_3001_4000=readRDS(file="H2_1_gfblup_prediction_all_3001_4000.rds")
+H2_1_gfblup_prediction_all_4001_5000=readRDS(file="H2_1_gfblup_prediction_all_4001_5000.rds")
+H2_1_gfblup_prediction_all_5001_6000=readRDS(file="H2_1_gfblup_prediction_all_5001_6000.rds")
+H2_1_gfblup_prediction_all_6001_7297=readRDS(file="H2_1_gfblup_prediction_all_6001_7297.rds")
+
+H2_1_gfblup_variances_all_1_1000=readRDS(file="H2_1_gfblup_variances_all_1_1000.rds")
+H2_1_gfblup_variances_all_1001_2000=readRDS(file="H2_1_gfblup_variances_all_1001_2000.rds")
+H2_1_gfblup_variances_all_2001_3000=readRDS(file="H2_1_gfblup_variances_all_2001_3000.rds")
+H2_1_gfblup_variances_all_3001_4000=readRDS(file="H2_1_gfblup_variances_all_3001_4000.rds")
+H2_1_gfblup_variances_all_4001_5000=readRDS(file="H2_1_gfblup_variances_all_4001_5000.rds")
+H2_1_gfblup_variances_all_5001_6000=readRDS(file="H2_1_gfblup_variances_all_5001_6000.rds")
+H2_1_gfblup_variances_all_6001_7297=readRDS(file="H2_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H2_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H2_1_gfblup_variances_all=rep(list(list()),cycles)
+H2_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_1_1000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_1001_2000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_2001_3000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_3001_4000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_4001_5000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_5001_6000[[r]])
+	H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_6001_7297[[r]])
+
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_1_1000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_1001_2000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_2001_3000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_3001_4000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_4001_5000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_5001_6000[[r]])
+	H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H2_1_gfblup_prediction_all,"H2_1_gfblup_prediction_all.rds")
+saveRDS(H2_1_gfblup_variances_all,"H2_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+H2_2_gblup_prediction_all_1_1000=readRDS(file="H2_2_gblup_prediction_all_1_1000.rds")
+H2_2_gblup_prediction_all_1001_2000=readRDS(file="H2_2_gblup_prediction_all_1001_2000.rds")
+H2_2_gblup_prediction_all_2001_3000=readRDS(file="H2_2_gblup_prediction_all_2001_3000.rds")
+H2_2_gblup_prediction_all_3001_4000=readRDS(file="H2_2_gblup_prediction_all_3001_4000.rds")
+H2_2_gblup_prediction_all_4001_5000=readRDS(file="H2_2_gblup_prediction_all_4001_5000.rds")
+H2_2_gblup_prediction_all_5001_6000=readRDS(file="H2_2_gblup_prediction_all_5001_6000.rds")
+H2_2_gblup_prediction_all_6001_7297=readRDS(file="H2_2_gblup_prediction_all_6001_7297.rds")
+H2_2_gblup_prediction_all=c(H2_2_gblup_prediction_all_1_1000,H2_2_gblup_prediction_all_1001_2000,H2_2_gblup_prediction_all_2001_3000,H2_2_gblup_prediction_all_3001_4000,H2_2_gblup_prediction_all_4001_5000,H2_2_gblup_prediction_all_5001_6000,H2_2_gblup_prediction_all_6001_7297)
+
+H2_2_gblup_variances_all_1_1000=readRDS(file="H2_2_gblup_variances_all_1_1000.rds")
+H2_2_gblup_variances_all_1001_2000=readRDS(file="H2_2_gblup_variances_all_1001_2000.rds")
+H2_2_gblup_variances_all_2001_3000=readRDS(file="H2_2_gblup_variances_all_2001_3000.rds")
+H2_2_gblup_variances_all_3001_4000=readRDS(file="H2_2_gblup_variances_all_3001_4000.rds")
+H2_2_gblup_variances_all_4001_5000=readRDS(file="H2_2_gblup_variances_all_4001_5000.rds")
+H2_2_gblup_variances_all_5001_6000=readRDS(file="H2_2_gblup_variances_all_5001_6000.rds")
+H2_2_gblup_variances_all_6001_7297=readRDS(file="H2_2_gblup_variances_all_6001_7297.rds")
+H2_2_gblup_variances_all=c(H2_2_gblup_variances_all_1_1000,H2_2_gblup_variances_all_1001_2000,H2_2_gblup_variances_all_2001_3000,H2_2_gblup_variances_all_3001_4000,H2_2_gblup_variances_all_4001_5000,H2_2_gblup_variances_all_5001_6000,H2_2_gblup_variances_all_6001_7297)
+
+saveRDS(H2_2_gblup_prediction_all,"H2_2_gblup_prediction_all.rds")
+saveRDS(H2_2_gblup_variances_all,"H2_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H2_2_gfblup_prediction_all_1_1000=readRDS(file="H2_2_gfblup_prediction_all_1_1000.rds")
+H2_2_gfblup_prediction_all_1001_2000=readRDS(file="H2_2_gfblup_prediction_all_1001_2000.rds")
+H2_2_gfblup_prediction_all_2001_3000=readRDS(file="H2_2_gfblup_prediction_all_2001_3000.rds")
+H2_2_gfblup_prediction_all_3001_4000=readRDS(file="H2_2_gfblup_prediction_all_3001_4000.rds")
+H2_2_gfblup_prediction_all_4001_5000=readRDS(file="H2_2_gfblup_prediction_all_4001_5000.rds")
+H2_2_gfblup_prediction_all_5001_6000=readRDS(file="H2_2_gfblup_prediction_all_5001_6000.rds")
+H2_2_gfblup_prediction_all_6001_7297=readRDS(file="H2_2_gfblup_prediction_all_6001_7297.rds")
+
+H2_2_gfblup_variances_all_1_1000=readRDS(file="H2_2_gfblup_variances_all_1_1000.rds")
+H2_2_gfblup_variances_all_1001_2000=readRDS(file="H2_2_gfblup_variances_all_1001_2000.rds")
+H2_2_gfblup_variances_all_2001_3000=readRDS(file="H2_2_gfblup_variances_all_2001_3000.rds")
+H2_2_gfblup_variances_all_3001_4000=readRDS(file="H2_2_gfblup_variances_all_3001_4000.rds")
+H2_2_gfblup_variances_all_4001_5000=readRDS(file="H2_2_gfblup_variances_all_4001_5000.rds")
+H2_2_gfblup_variances_all_5001_6000=readRDS(file="H2_2_gfblup_variances_all_5001_6000.rds")
+H2_2_gfblup_variances_all_6001_7297=readRDS(file="H2_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H2_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H2_2_gfblup_variances_all=rep(list(list()),cycles)
+H2_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_1_1000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_1001_2000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_2001_3000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_3001_4000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_4001_5000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_5001_6000[[r]])
+	H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_6001_7297[[r]])
+
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_1_1000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_1001_2000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_2001_3000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_3001_4000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_4001_5000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_5001_6000[[r]])
+	H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H2_2_gfblup_prediction_all,"H2_2_gfblup_prediction_all.rds")
+saveRDS(H2_2_gfblup_variances_all,"H2_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+H2_3_gblup_prediction_all_1_1000=readRDS(file="H2_3_gblup_prediction_all_1_1000.rds")
+H2_3_gblup_prediction_all_1001_2000=readRDS(file="H2_3_gblup_prediction_all_1001_2000.rds")
+H2_3_gblup_prediction_all_2001_3000=readRDS(file="H2_3_gblup_prediction_all_2001_3000.rds")
+H2_3_gblup_prediction_all_3001_4000=readRDS(file="H2_3_gblup_prediction_all_3001_4000.rds")
+H2_3_gblup_prediction_all_4001_5000=readRDS(file="H2_3_gblup_prediction_all_4001_5000.rds")
+H2_3_gblup_prediction_all_5001_6000=readRDS(file="H2_3_gblup_prediction_all_5001_6000.rds")
+H2_3_gblup_prediction_all_6001_7297=readRDS(file="H2_3_gblup_prediction_all_6001_7297.rds")
+H2_3_gblup_prediction_all=c(H2_3_gblup_prediction_all_1_1000,H2_3_gblup_prediction_all_1001_2000,H2_3_gblup_prediction_all_2001_3000,H2_3_gblup_prediction_all_3001_4000,H2_3_gblup_prediction_all_4001_5000,H2_3_gblup_prediction_all_5001_6000,H2_3_gblup_prediction_all_6001_7297)
+
+H2_3_gblup_variances_all_1_1000=readRDS(file="H2_3_gblup_variances_all_1_1000.rds")
+H2_3_gblup_variances_all_1001_2000=readRDS(file="H2_3_gblup_variances_all_1001_2000.rds")
+H2_3_gblup_variances_all_2001_3000=readRDS(file="H2_3_gblup_variances_all_2001_3000.rds")
+H2_3_gblup_variances_all_3001_4000=readRDS(file="H2_3_gblup_variances_all_3001_4000.rds")
+H2_3_gblup_variances_all_4001_5000=readRDS(file="H2_3_gblup_variances_all_4001_5000.rds")
+H2_3_gblup_variances_all_5001_6000=readRDS(file="H2_3_gblup_variances_all_5001_6000.rds")
+H2_3_gblup_variances_all_6001_7297=readRDS(file="H2_3_gblup_variances_all_6001_7297.rds")
+H2_3_gblup_variances_all=c(H2_3_gblup_variances_all_1_1000,H2_3_gblup_variances_all_1001_2000,H2_3_gblup_variances_all_2001_3000,H2_3_gblup_variances_all_3001_4000,H2_3_gblup_variances_all_4001_5000,H2_3_gblup_variances_all_5001_6000,H2_3_gblup_variances_all_6001_7297)
+
+saveRDS(H2_3_gblup_prediction_all,"H2_3_gblup_prediction_all.rds")
+saveRDS(H2_3_gblup_variances_all,"H2_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H2_3_gfblup_prediction_all_1_1000=readRDS(file="H2_3_gfblup_prediction_all_1_1000.rds")
+H2_3_gfblup_prediction_all_1001_2000=readRDS(file="H2_3_gfblup_prediction_all_1001_2000.rds")
+H2_3_gfblup_prediction_all_2001_3000=readRDS(file="H2_3_gfblup_prediction_all_2001_3000.rds")
+H2_3_gfblup_prediction_all_3001_4000=readRDS(file="H2_3_gfblup_prediction_all_3001_4000.rds")
+H2_3_gfblup_prediction_all_4001_5000=readRDS(file="H2_3_gfblup_prediction_all_4001_5000.rds")
+H2_3_gfblup_prediction_all_5001_6000=readRDS(file="H2_3_gfblup_prediction_all_5001_6000.rds")
+H2_3_gfblup_prediction_all_6001_7297=readRDS(file="H2_3_gfblup_prediction_all_6001_7297.rds")
+
+H2_3_gfblup_variances_all_1_1000=readRDS(file="H2_3_gfblup_variances_all_1_1000.rds")
+H2_3_gfblup_variances_all_1001_2000=readRDS(file="H2_3_gfblup_variances_all_1001_2000.rds")
+H2_3_gfblup_variances_all_2001_3000=readRDS(file="H2_3_gfblup_variances_all_2001_3000.rds")
+H2_3_gfblup_variances_all_3001_4000=readRDS(file="H2_3_gfblup_variances_all_3001_4000.rds")
+H2_3_gfblup_variances_all_4001_5000=readRDS(file="H2_3_gfblup_variances_all_4001_5000.rds")
+H2_3_gfblup_variances_all_5001_6000=readRDS(file="H2_3_gfblup_variances_all_5001_6000.rds")
+H2_3_gfblup_variances_all_6001_7297=readRDS(file="H2_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H2_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H2_3_gfblup_variances_all=rep(list(list()),cycles)
+H2_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_1_1000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_1001_2000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_2001_3000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_3001_4000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_4001_5000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_5001_6000[[r]])
+	H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_6001_7297[[r]])
+
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_1_1000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_1001_2000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_2001_3000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_3001_4000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_4001_5000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_5001_6000[[r]])
+	H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H2_3_gfblup_prediction_all,"H2_3_gfblup_prediction_all.rds")
+saveRDS(H2_3_gfblup_variances_all,"H2_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H3_1_gblup_prediction_all_1_1000=readRDS(file="H3_1_gblup_prediction_all_1_1000.rds")
+H3_1_gblup_prediction_all_1001_2000=readRDS(file="H3_1_gblup_prediction_all_1001_2000.rds")
+H3_1_gblup_prediction_all_2001_3000=readRDS(file="H3_1_gblup_prediction_all_2001_3000.rds")
+H3_1_gblup_prediction_all_3001_4000=readRDS(file="H3_1_gblup_prediction_all_3001_4000.rds")
+H3_1_gblup_prediction_all_4001_5000=readRDS(file="H3_1_gblup_prediction_all_4001_5000.rds")
+H3_1_gblup_prediction_all_5001_6000=readRDS(file="H3_1_gblup_prediction_all_5001_6000.rds")
+H3_1_gblup_prediction_all_6001_7297=readRDS(file="H3_1_gblup_prediction_all_6001_7297.rds")
+H3_1_gblup_prediction_all=c(H3_1_gblup_prediction_all_1_1000,H3_1_gblup_prediction_all_1001_2000,H3_1_gblup_prediction_all_2001_3000,H3_1_gblup_prediction_all_3001_4000,H3_1_gblup_prediction_all_4001_5000,H3_1_gblup_prediction_all_5001_6000,H3_1_gblup_prediction_all_6001_7297)
+
+H3_1_gblup_variances_all_1_1000=readRDS(file="H3_1_gblup_variances_all_1_1000.rds")
+H3_1_gblup_variances_all_1001_2000=readRDS(file="H3_1_gblup_variances_all_1001_2000.rds")
+H3_1_gblup_variances_all_2001_3000=readRDS(file="H3_1_gblup_variances_all_2001_3000.rds")
+H3_1_gblup_variances_all_3001_4000=readRDS(file="H3_1_gblup_variances_all_3001_4000.rds")
+H3_1_gblup_variances_all_4001_5000=readRDS(file="H3_1_gblup_variances_all_4001_5000.rds")
+H3_1_gblup_variances_all_5001_6000=readRDS(file="H3_1_gblup_variances_all_5001_6000.rds")
+H3_1_gblup_variances_all_6001_7297=readRDS(file="H3_1_gblup_variances_all_6001_7297.rds")
+H3_1_gblup_variances_all=c(H3_1_gblup_variances_all_1_1000,H3_1_gblup_variances_all_1001_2000,H3_1_gblup_variances_all_2001_3000,H3_1_gblup_variances_all_3001_4000,H3_1_gblup_variances_all_4001_5000,H3_1_gblup_variances_all_5001_6000,H3_1_gblup_variances_all_6001_7297)
+
+saveRDS(H3_1_gblup_prediction_all,"H3_1_gblup_prediction_all.rds")
+saveRDS(H3_1_gblup_variances_all,"H3_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H3_1_gfblup_prediction_all_1_1000=readRDS(file="H3_1_gfblup_prediction_all_1_1000.rds")
+H3_1_gfblup_prediction_all_1001_2000=readRDS(file="H3_1_gfblup_prediction_all_1001_2000.rds")
+H3_1_gfblup_prediction_all_2001_3000=readRDS(file="H3_1_gfblup_prediction_all_2001_3000.rds")
+H3_1_gfblup_prediction_all_3001_4000=readRDS(file="H3_1_gfblup_prediction_all_3001_4000.rds")
+H3_1_gfblup_prediction_all_4001_5000=readRDS(file="H3_1_gfblup_prediction_all_4001_5000.rds")
+H3_1_gfblup_prediction_all_5001_6000=readRDS(file="H3_1_gfblup_prediction_all_5001_6000.rds")
+H3_1_gfblup_prediction_all_6001_7297=readRDS(file="H3_1_gfblup_prediction_all_6001_7297.rds")
+
+H3_1_gfblup_variances_all_1_1000=readRDS(file="H3_1_gfblup_variances_all_1_1000.rds")
+H3_1_gfblup_variances_all_1001_2000=readRDS(file="H3_1_gfblup_variances_all_1001_2000.rds")
+H3_1_gfblup_variances_all_2001_3000=readRDS(file="H3_1_gfblup_variances_all_2001_3000.rds")
+H3_1_gfblup_variances_all_3001_4000=readRDS(file="H3_1_gfblup_variances_all_3001_4000.rds")
+H3_1_gfblup_variances_all_4001_5000=readRDS(file="H3_1_gfblup_variances_all_4001_5000.rds")
+H3_1_gfblup_variances_all_5001_6000=readRDS(file="H3_1_gfblup_variances_all_5001_6000.rds")
+H3_1_gfblup_variances_all_6001_7297=readRDS(file="H3_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H3_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H3_1_gfblup_variances_all=rep(list(list()),cycles)
+H3_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_1_1000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_1001_2000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_2001_3000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_3001_4000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_4001_5000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_5001_6000[[r]])
+	H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_6001_7297[[r]])
+
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_1_1000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_1001_2000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_2001_3000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_3001_4000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_4001_5000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_5001_6000[[r]])
+	H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H3_1_gfblup_prediction_all,"H3_1_gfblup_prediction_all.rds")
+saveRDS(H3_1_gfblup_variances_all,"H3_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+H3_2_gblup_prediction_all_1_1000=readRDS(file="H3_2_gblup_prediction_all_1_1000.rds")
+H3_2_gblup_prediction_all_1001_2000=readRDS(file="H3_2_gblup_prediction_all_1001_2000.rds")
+H3_2_gblup_prediction_all_2001_3000=readRDS(file="H3_2_gblup_prediction_all_2001_3000.rds")
+H3_2_gblup_prediction_all_3001_4000=readRDS(file="H3_2_gblup_prediction_all_3001_4000.rds")
+H3_2_gblup_prediction_all_4001_5000=readRDS(file="H3_2_gblup_prediction_all_4001_5000.rds")
+H3_2_gblup_prediction_all_5001_6000=readRDS(file="H3_2_gblup_prediction_all_5001_6000.rds")
+H3_2_gblup_prediction_all_6001_7297=readRDS(file="H3_2_gblup_prediction_all_6001_7297.rds")
+H3_2_gblup_prediction_all=c(H3_2_gblup_prediction_all_1_1000,H3_2_gblup_prediction_all_1001_2000,H3_2_gblup_prediction_all_2001_3000,H3_2_gblup_prediction_all_3001_4000,H3_2_gblup_prediction_all_4001_5000,H3_2_gblup_prediction_all_5001_6000,H3_2_gblup_prediction_all_6001_7297)
+
+H3_2_gblup_variances_all_1_1000=readRDS(file="H3_2_gblup_variances_all_1_1000.rds")
+H3_2_gblup_variances_all_1001_2000=readRDS(file="H3_2_gblup_variances_all_1001_2000.rds")
+H3_2_gblup_variances_all_2001_3000=readRDS(file="H3_2_gblup_variances_all_2001_3000.rds")
+H3_2_gblup_variances_all_3001_4000=readRDS(file="H3_2_gblup_variances_all_3001_4000.rds")
+H3_2_gblup_variances_all_4001_5000=readRDS(file="H3_2_gblup_variances_all_4001_5000.rds")
+H3_2_gblup_variances_all_5001_6000=readRDS(file="H3_2_gblup_variances_all_5001_6000.rds")
+H3_2_gblup_variances_all_6001_7297=readRDS(file="H3_2_gblup_variances_all_6001_7297.rds")
+H3_2_gblup_variances_all=c(H3_2_gblup_variances_all_1_1000,H3_2_gblup_variances_all_1001_2000,H3_2_gblup_variances_all_2001_3000,H3_2_gblup_variances_all_3001_4000,H3_2_gblup_variances_all_4001_5000,H3_2_gblup_variances_all_5001_6000,H3_2_gblup_variances_all_6001_7297)
+
+saveRDS(H3_2_gblup_prediction_all,"H3_2_gblup_prediction_all.rds")
+saveRDS(H3_2_gblup_variances_all,"H3_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H3_2_gfblup_prediction_all_1_1000=readRDS(file="H3_2_gfblup_prediction_all_1_1000.rds")
+H3_2_gfblup_prediction_all_1001_2000=readRDS(file="H3_2_gfblup_prediction_all_1001_2000.rds")
+H3_2_gfblup_prediction_all_2001_3000=readRDS(file="H3_2_gfblup_prediction_all_2001_3000.rds")
+H3_2_gfblup_prediction_all_3001_4000=readRDS(file="H3_2_gfblup_prediction_all_3001_4000.rds")
+H3_2_gfblup_prediction_all_4001_5000=readRDS(file="H3_2_gfblup_prediction_all_4001_5000.rds")
+H3_2_gfblup_prediction_all_5001_6000=readRDS(file="H3_2_gfblup_prediction_all_5001_6000.rds")
+H3_2_gfblup_prediction_all_6001_7297=readRDS(file="H3_2_gfblup_prediction_all_6001_7297.rds")
+
+H3_2_gfblup_variances_all_1_1000=readRDS(file="H3_2_gfblup_variances_all_1_1000.rds")
+H3_2_gfblup_variances_all_1001_2000=readRDS(file="H3_2_gfblup_variances_all_1001_2000.rds")
+H3_2_gfblup_variances_all_2001_3000=readRDS(file="H3_2_gfblup_variances_all_2001_3000.rds")
+H3_2_gfblup_variances_all_3001_4000=readRDS(file="H3_2_gfblup_variances_all_3001_4000.rds")
+H3_2_gfblup_variances_all_4001_5000=readRDS(file="H3_2_gfblup_variances_all_4001_5000.rds")
+H3_2_gfblup_variances_all_5001_6000=readRDS(file="H3_2_gfblup_variances_all_5001_6000.rds")
+H3_2_gfblup_variances_all_6001_7297=readRDS(file="H3_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H3_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H3_2_gfblup_variances_all=rep(list(list()),cycles)
+H3_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_1_1000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_1001_2000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_2001_3000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_3001_4000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_4001_5000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_5001_6000[[r]])
+	H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_6001_7297[[r]])
+
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_1_1000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_1001_2000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_2001_3000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_3001_4000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_4001_5000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_5001_6000[[r]])
+	H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H3_2_gfblup_prediction_all,"H3_2_gfblup_prediction_all.rds")
+saveRDS(H3_2_gfblup_variances_all,"H3_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+H3_3_gblup_prediction_all_1_1000=readRDS(file="H3_3_gblup_prediction_all_1_1000.rds")
+H3_3_gblup_prediction_all_1001_2000=readRDS(file="H3_3_gblup_prediction_all_1001_2000.rds")
+H3_3_gblup_prediction_all_2001_3000=readRDS(file="H3_3_gblup_prediction_all_2001_3000.rds")
+H3_3_gblup_prediction_all_3001_4000=readRDS(file="H3_3_gblup_prediction_all_3001_4000.rds")
+H3_3_gblup_prediction_all_4001_5000=readRDS(file="H3_3_gblup_prediction_all_4001_5000.rds")
+H3_3_gblup_prediction_all_5001_6000=readRDS(file="H3_3_gblup_prediction_all_5001_6000.rds")
+H3_3_gblup_prediction_all_6001_7297=readRDS(file="H3_3_gblup_prediction_all_6001_7297.rds")
+H3_3_gblup_prediction_all=c(H3_3_gblup_prediction_all_1_1000,H3_3_gblup_prediction_all_1001_2000,H3_3_gblup_prediction_all_2001_3000,H3_3_gblup_prediction_all_3001_4000,H3_3_gblup_prediction_all_4001_5000,H3_3_gblup_prediction_all_5001_6000,H3_3_gblup_prediction_all_6001_7297)
+
+H3_3_gblup_variances_all_1_1000=readRDS(file="H3_3_gblup_variances_all_1_1000.rds")
+H3_3_gblup_variances_all_1001_2000=readRDS(file="H3_3_gblup_variances_all_1001_2000.rds")
+H3_3_gblup_variances_all_2001_3000=readRDS(file="H3_3_gblup_variances_all_2001_3000.rds")
+H3_3_gblup_variances_all_3001_4000=readRDS(file="H3_3_gblup_variances_all_3001_4000.rds")
+H3_3_gblup_variances_all_4001_5000=readRDS(file="H3_3_gblup_variances_all_4001_5000.rds")
+H3_3_gblup_variances_all_5001_6000=readRDS(file="H3_3_gblup_variances_all_5001_6000.rds")
+H3_3_gblup_variances_all_6001_7297=readRDS(file="H3_3_gblup_variances_all_6001_7297.rds")
+H3_3_gblup_variances_all=c(H3_3_gblup_variances_all_1_1000,H3_3_gblup_variances_all_1001_2000,H3_3_gblup_variances_all_2001_3000,H3_3_gblup_variances_all_3001_4000,H3_3_gblup_variances_all_4001_5000,H3_3_gblup_variances_all_5001_6000,H3_3_gblup_variances_all_6001_7297)
+
+saveRDS(H3_3_gblup_prediction_all,"H3_3_gblup_prediction_all.rds")
+saveRDS(H3_3_gblup_variances_all,"H3_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H3_3_gfblup_prediction_all_1_1000=readRDS(file="H3_3_gfblup_prediction_all_1_1000.rds")
+H3_3_gfblup_prediction_all_1001_2000=readRDS(file="H3_3_gfblup_prediction_all_1001_2000.rds")
+H3_3_gfblup_prediction_all_2001_3000=readRDS(file="H3_3_gfblup_prediction_all_2001_3000.rds")
+H3_3_gfblup_prediction_all_3001_4000=readRDS(file="H3_3_gfblup_prediction_all_3001_4000.rds")
+H3_3_gfblup_prediction_all_4001_5000=readRDS(file="H3_3_gfblup_prediction_all_4001_5000.rds")
+H3_3_gfblup_prediction_all_5001_6000=readRDS(file="H3_3_gfblup_prediction_all_5001_6000.rds")
+H3_3_gfblup_prediction_all_6001_7297=readRDS(file="H3_3_gfblup_prediction_all_6001_7297.rds")
+
+H3_3_gfblup_variances_all_1_1000=readRDS(file="H3_3_gfblup_variances_all_1_1000.rds")
+H3_3_gfblup_variances_all_1001_2000=readRDS(file="H3_3_gfblup_variances_all_1001_2000.rds")
+H3_3_gfblup_variances_all_2001_3000=readRDS(file="H3_3_gfblup_variances_all_2001_3000.rds")
+H3_3_gfblup_variances_all_3001_4000=readRDS(file="H3_3_gfblup_variances_all_3001_4000.rds")
+H3_3_gfblup_variances_all_4001_5000=readRDS(file="H3_3_gfblup_variances_all_4001_5000.rds")
+H3_3_gfblup_variances_all_5001_6000=readRDS(file="H3_3_gfblup_variances_all_5001_6000.rds")
+H3_3_gfblup_variances_all_6001_7297=readRDS(file="H3_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H3_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H3_3_gfblup_variances_all=rep(list(list()),cycles)
+H3_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_1_1000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_1001_2000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_2001_3000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_3001_4000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_4001_5000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_5001_6000[[r]])
+	H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_6001_7297[[r]])
+
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_1_1000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_1001_2000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_2001_3000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_3001_4000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_4001_5000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_5001_6000[[r]])
+	H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H3_3_gfblup_prediction_all,"H3_3_gfblup_prediction_all.rds")
+saveRDS(H3_3_gfblup_variances_all,"H3_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+H4_1_gblup_prediction_all_1_1000=readRDS(file="H4_1_gblup_prediction_all_1_1000.rds")
+H4_1_gblup_prediction_all_1001_2000=readRDS(file="H4_1_gblup_prediction_all_1001_2000.rds")
+H4_1_gblup_prediction_all_2001_3000=readRDS(file="H4_1_gblup_prediction_all_2001_3000.rds")
+H4_1_gblup_prediction_all_3001_4000=readRDS(file="H4_1_gblup_prediction_all_3001_4000.rds")
+H4_1_gblup_prediction_all_4001_5000=readRDS(file="H4_1_gblup_prediction_all_4001_5000.rds")
+H4_1_gblup_prediction_all_5001_6000=readRDS(file="H4_1_gblup_prediction_all_5001_6000.rds")
+H4_1_gblup_prediction_all_6001_7297=readRDS(file="H4_1_gblup_prediction_all_6001_7297.rds")
+H4_1_gblup_prediction_all=c(H4_1_gblup_prediction_all_1_1000,H4_1_gblup_prediction_all_1001_2000,H4_1_gblup_prediction_all_2001_3000,H4_1_gblup_prediction_all_3001_4000,H4_1_gblup_prediction_all_4001_5000,H4_1_gblup_prediction_all_5001_6000,H4_1_gblup_prediction_all_6001_7297)
+
+H4_1_gblup_variances_all_1_1000=readRDS(file="H4_1_gblup_variances_all_1_1000.rds")
+H4_1_gblup_variances_all_1001_2000=readRDS(file="H4_1_gblup_variances_all_1001_2000.rds")
+H4_1_gblup_variances_all_2001_3000=readRDS(file="H4_1_gblup_variances_all_2001_3000.rds")
+H4_1_gblup_variances_all_3001_4000=readRDS(file="H4_1_gblup_variances_all_3001_4000.rds")
+H4_1_gblup_variances_all_4001_5000=readRDS(file="H4_1_gblup_variances_all_4001_5000.rds")
+H4_1_gblup_variances_all_5001_6000=readRDS(file="H4_1_gblup_variances_all_5001_6000.rds")
+H4_1_gblup_variances_all_6001_7297=readRDS(file="H4_1_gblup_variances_all_6001_7297.rds")
+H4_1_gblup_variances_all=c(H4_1_gblup_variances_all_1_1000,H4_1_gblup_variances_all_1001_2000,H4_1_gblup_variances_all_2001_3000,H4_1_gblup_variances_all_3001_4000,H4_1_gblup_variances_all_4001_5000,H4_1_gblup_variances_all_5001_6000,H4_1_gblup_variances_all_6001_7297)
+
+saveRDS(H4_1_gblup_prediction_all,"H4_1_gblup_prediction_all.rds")
+saveRDS(H4_1_gblup_variances_all,"H4_1_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H4_1_gfblup_prediction_all_1_1000=readRDS(file="H4_1_gfblup_prediction_all_1_1000.rds")
+H4_1_gfblup_prediction_all_1001_2000=readRDS(file="H4_1_gfblup_prediction_all_1001_2000.rds")
+H4_1_gfblup_prediction_all_2001_3000=readRDS(file="H4_1_gfblup_prediction_all_2001_3000.rds")
+H4_1_gfblup_prediction_all_3001_4000=readRDS(file="H4_1_gfblup_prediction_all_3001_4000.rds")
+H4_1_gfblup_prediction_all_4001_5000=readRDS(file="H4_1_gfblup_prediction_all_4001_5000.rds")
+H4_1_gfblup_prediction_all_5001_6000=readRDS(file="H4_1_gfblup_prediction_all_5001_6000.rds")
+H4_1_gfblup_prediction_all_6001_7297=readRDS(file="H4_1_gfblup_prediction_all_6001_7297.rds")
+
+H4_1_gfblup_variances_all_1_1000=readRDS(file="H4_1_gfblup_variances_all_1_1000.rds")
+H4_1_gfblup_variances_all_1001_2000=readRDS(file="H4_1_gfblup_variances_all_1001_2000.rds")
+H4_1_gfblup_variances_all_2001_3000=readRDS(file="H4_1_gfblup_variances_all_2001_3000.rds")
+H4_1_gfblup_variances_all_3001_4000=readRDS(file="H4_1_gfblup_variances_all_3001_4000.rds")
+H4_1_gfblup_variances_all_4001_5000=readRDS(file="H4_1_gfblup_variances_all_4001_5000.rds")
+H4_1_gfblup_variances_all_5001_6000=readRDS(file="H4_1_gfblup_variances_all_5001_6000.rds")
+H4_1_gfblup_variances_all_6001_7297=readRDS(file="H4_1_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H4_1_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H4_1_gfblup_variances_all=rep(list(list()),cycles)
+H4_1_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_1_1000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_1001_2000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_2001_3000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_3001_4000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_4001_5000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_5001_6000[[r]])
+	H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_6001_7297[[r]])
+
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_1_1000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_1001_2000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_2001_3000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_3001_4000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_4001_5000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_5001_6000[[r]])
+	H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H4_1_gfblup_prediction_all,"H4_1_gfblup_prediction_all.rds")
+saveRDS(H4_1_gfblup_variances_all,"H4_1_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+H4_2_gblup_prediction_all_1_1000=readRDS(file="H4_2_gblup_prediction_all_1_1000.rds")
+H4_2_gblup_prediction_all_1001_2000=readRDS(file="H4_2_gblup_prediction_all_1001_2000.rds")
+H4_2_gblup_prediction_all_2001_3000=readRDS(file="H4_2_gblup_prediction_all_2001_3000.rds")
+H4_2_gblup_prediction_all_3001_4000=readRDS(file="H4_2_gblup_prediction_all_3001_4000.rds")
+H4_2_gblup_prediction_all_4001_5000=readRDS(file="H4_2_gblup_prediction_all_4001_5000.rds")
+H4_2_gblup_prediction_all_5001_6000=readRDS(file="H4_2_gblup_prediction_all_5001_6000.rds")
+H4_2_gblup_prediction_all_6001_7297=readRDS(file="H4_2_gblup_prediction_all_6001_7297.rds")
+H4_2_gblup_prediction_all=c(H4_2_gblup_prediction_all_1_1000,H4_2_gblup_prediction_all_1001_2000,H4_2_gblup_prediction_all_2001_3000,H4_2_gblup_prediction_all_3001_4000,H4_2_gblup_prediction_all_4001_5000,H4_2_gblup_prediction_all_5001_6000,H4_2_gblup_prediction_all_6001_7297)
+
+H4_2_gblup_variances_all_1_1000=readRDS(file="H4_2_gblup_variances_all_1_1000.rds")
+H4_2_gblup_variances_all_1001_2000=readRDS(file="H4_2_gblup_variances_all_1001_2000.rds")
+H4_2_gblup_variances_all_2001_3000=readRDS(file="H4_2_gblup_variances_all_2001_3000.rds")
+H4_2_gblup_variances_all_3001_4000=readRDS(file="H4_2_gblup_variances_all_3001_4000.rds")
+H4_2_gblup_variances_all_4001_5000=readRDS(file="H4_2_gblup_variances_all_4001_5000.rds")
+H4_2_gblup_variances_all_5001_6000=readRDS(file="H4_2_gblup_variances_all_5001_6000.rds")
+H4_2_gblup_variances_all_6001_7297=readRDS(file="H4_2_gblup_variances_all_6001_7297.rds")
+H4_2_gblup_variances_all=c(H4_2_gblup_variances_all_1_1000,H4_2_gblup_variances_all_1001_2000,H4_2_gblup_variances_all_2001_3000,H4_2_gblup_variances_all_3001_4000,H4_2_gblup_variances_all_4001_5000,H4_2_gblup_variances_all_5001_6000,H4_2_gblup_variances_all_6001_7297)
+
+saveRDS(H4_2_gblup_prediction_all,"H4_2_gblup_prediction_all.rds")
+saveRDS(H4_2_gblup_variances_all,"H4_2_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H4_2_gfblup_prediction_all_1_1000=readRDS(file="H4_2_gfblup_prediction_all_1_1000.rds")
+H4_2_gfblup_prediction_all_1001_2000=readRDS(file="H4_2_gfblup_prediction_all_1001_2000.rds")
+H4_2_gfblup_prediction_all_2001_3000=readRDS(file="H4_2_gfblup_prediction_all_2001_3000.rds")
+H4_2_gfblup_prediction_all_3001_4000=readRDS(file="H4_2_gfblup_prediction_all_3001_4000.rds")
+H4_2_gfblup_prediction_all_4001_5000=readRDS(file="H4_2_gfblup_prediction_all_4001_5000.rds")
+H4_2_gfblup_prediction_all_5001_6000=readRDS(file="H4_2_gfblup_prediction_all_5001_6000.rds")
+H4_2_gfblup_prediction_all_6001_7297=readRDS(file="H4_2_gfblup_prediction_all_6001_7297.rds")
+
+H4_2_gfblup_variances_all_1_1000=readRDS(file="H4_2_gfblup_variances_all_1_1000.rds")
+H4_2_gfblup_variances_all_1001_2000=readRDS(file="H4_2_gfblup_variances_all_1001_2000.rds")
+H4_2_gfblup_variances_all_2001_3000=readRDS(file="H4_2_gfblup_variances_all_2001_3000.rds")
+H4_2_gfblup_variances_all_3001_4000=readRDS(file="H4_2_gfblup_variances_all_3001_4000.rds")
+H4_2_gfblup_variances_all_4001_5000=readRDS(file="H4_2_gfblup_variances_all_4001_5000.rds")
+H4_2_gfblup_variances_all_5001_6000=readRDS(file="H4_2_gfblup_variances_all_5001_6000.rds")
+H4_2_gfblup_variances_all_6001_7297=readRDS(file="H4_2_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H4_2_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H4_2_gfblup_variances_all=rep(list(list()),cycles)
+H4_2_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_1_1000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_1001_2000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_2001_3000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_3001_4000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_4001_5000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_5001_6000[[r]])
+	H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_6001_7297[[r]])
+
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_1_1000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_1001_2000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_2001_3000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_3001_4000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_4001_5000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_5001_6000[[r]])
+	H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H4_2_gfblup_prediction_all,"H4_2_gfblup_prediction_all.rds")
+saveRDS(H4_2_gfblup_variances_all,"H4_2_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+H4_3_gblup_prediction_all_1_1000=readRDS(file="H4_3_gblup_prediction_all_1_1000.rds")
+H4_3_gblup_prediction_all_1001_2000=readRDS(file="H4_3_gblup_prediction_all_1001_2000.rds")
+H4_3_gblup_prediction_all_2001_3000=readRDS(file="H4_3_gblup_prediction_all_2001_3000.rds")
+H4_3_gblup_prediction_all_3001_4000=readRDS(file="H4_3_gblup_prediction_all_3001_4000.rds")
+H4_3_gblup_prediction_all_4001_5000=readRDS(file="H4_3_gblup_prediction_all_4001_5000.rds")
+H4_3_gblup_prediction_all_5001_6000=readRDS(file="H4_3_gblup_prediction_all_5001_6000.rds")
+H4_3_gblup_prediction_all_6001_7297=readRDS(file="H4_3_gblup_prediction_all_6001_7297.rds")
+H4_3_gblup_prediction_all=c(H4_3_gblup_prediction_all_1_1000,H4_3_gblup_prediction_all_1001_2000,H4_3_gblup_prediction_all_2001_3000,H4_3_gblup_prediction_all_3001_4000,H4_3_gblup_prediction_all_4001_5000,H4_3_gblup_prediction_all_5001_6000,H4_3_gblup_prediction_all_6001_7297)
+
+H4_3_gblup_variances_all_1_1000=readRDS(file="H4_3_gblup_variances_all_1_1000.rds")
+H4_3_gblup_variances_all_1001_2000=readRDS(file="H4_3_gblup_variances_all_1001_2000.rds")
+H4_3_gblup_variances_all_2001_3000=readRDS(file="H4_3_gblup_variances_all_2001_3000.rds")
+H4_3_gblup_variances_all_3001_4000=readRDS(file="H4_3_gblup_variances_all_3001_4000.rds")
+H4_3_gblup_variances_all_4001_5000=readRDS(file="H4_3_gblup_variances_all_4001_5000.rds")
+H4_3_gblup_variances_all_5001_6000=readRDS(file="H4_3_gblup_variances_all_5001_6000.rds")
+H4_3_gblup_variances_all_6001_7297=readRDS(file="H4_3_gblup_variances_all_6001_7297.rds")
+H4_3_gblup_variances_all=c(H4_3_gblup_variances_all_1_1000,H4_3_gblup_variances_all_1001_2000,H4_3_gblup_variances_all_2001_3000,H4_3_gblup_variances_all_3001_4000,H4_3_gblup_variances_all_4001_5000,H4_3_gblup_variances_all_5001_6000,H4_3_gblup_variances_all_6001_7297)
+
+saveRDS(H4_3_gblup_prediction_all,"H4_3_gblup_prediction_all.rds")
+saveRDS(H4_3_gblup_variances_all,"H4_3_gblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+H4_3_gfblup_prediction_all_1_1000=readRDS(file="H4_3_gfblup_prediction_all_1_1000.rds")
+H4_3_gfblup_prediction_all_1001_2000=readRDS(file="H4_3_gfblup_prediction_all_1001_2000.rds")
+H4_3_gfblup_prediction_all_2001_3000=readRDS(file="H4_3_gfblup_prediction_all_2001_3000.rds")
+H4_3_gfblup_prediction_all_3001_4000=readRDS(file="H4_3_gfblup_prediction_all_3001_4000.rds")
+H4_3_gfblup_prediction_all_4001_5000=readRDS(file="H4_3_gfblup_prediction_all_4001_5000.rds")
+H4_3_gfblup_prediction_all_5001_6000=readRDS(file="H4_3_gfblup_prediction_all_5001_6000.rds")
+H4_3_gfblup_prediction_all_6001_7297=readRDS(file="H4_3_gfblup_prediction_all_6001_7297.rds")
+
+H4_3_gfblup_variances_all_1_1000=readRDS(file="H4_3_gfblup_variances_all_1_1000.rds")
+H4_3_gfblup_variances_all_1001_2000=readRDS(file="H4_3_gfblup_variances_all_1001_2000.rds")
+H4_3_gfblup_variances_all_2001_3000=readRDS(file="H4_3_gfblup_variances_all_2001_3000.rds")
+H4_3_gfblup_variances_all_3001_4000=readRDS(file="H4_3_gfblup_variances_all_3001_4000.rds")
+H4_3_gfblup_variances_all_4001_5000=readRDS(file="H4_3_gfblup_variances_all_4001_5000.rds")
+H4_3_gfblup_variances_all_5001_6000=readRDS(file="H4_3_gfblup_variances_all_5001_6000.rds")
+H4_3_gfblup_variances_all_6001_7297=readRDS(file="H4_3_gfblup_variances_all_6001_7297.rds")
+
+cycles=length(H4_3_gfblup_prediction_all_1_1000)
+n_folds <- 8
+
+H4_3_gfblup_variances_all=rep(list(list()),cycles)
+H4_3_gfblup_prediction_all=rep(list(list()),cycles)
+
+for(r in 1:cycles)
+{
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_1_1000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_1001_2000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_2001_3000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_3001_4000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_4001_5000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_5001_6000[[r]])
+	H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_6001_7297[[r]])
+
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_1_1000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_1001_2000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_2001_3000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_3001_4000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_4001_5000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_5001_6000[[r]])
+	H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_6001_7297[[r]])
+
+}
+
+saveRDS(H4_3_gfblup_prediction_all,"H4_3_gfblup_prediction_all.rds")
+saveRDS(H4_3_gfblup_variances_all,"H4_3_gfblup_variances_all.rds")
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/code/using_GO/psii/gblup_vs_gfblup_using_go_analysis1.R b/code/using_GO/psii/gblup_vs_gfblup_using_go_analysis1.R
index e02a732..e0cc750 100644
--- a/code/using_GO/psii/gblup_vs_gfblup_using_go_analysis1.R
+++ b/code/using_GO/psii/gblup_vs_gfblup_using_go_analysis1.R
@@ -2,7 +2,24 @@
 ##################################################################################################################################
 #	A	N	A	L	Y	S	I	S
 ##################################################################################################################################
-setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/psii/8fold/")
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+setwd(paste0(wdir,"/",wd,"/8fold/"));
+#################################################################################################################
 require(GO.db)
 
 L2_2_gblup_variances_all=readRDS(file="./L2_2_gblup_variances_all.rds")
@@ -110,42 +127,3 @@ saveRDS(L2_2_all,"L2_2_all_analysis1.rds")
 write.table(L2_2_all_important, file="L2_2_gblup_vs_gfblup_all_using_go_important_analysis1.tbl", sep = "\t", dec = ".",row.names = TRUE, col.names = TRUE)
 saveRDS(L2_2_all_important,"L2_2_all_important_analysis1.rds")
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-##################################################################################################################################
-#	DIFFERENCE in RANDOM VS BIOLOGY DRIVEN SUBSET OF MARKERS (This doesn't seem to help alot, so no need to show this plot)
-##################################################################################################################################
-goid_important=rownames(L2_2_all_important)
-go_all_markers_filtered_important=go_all_markers_filtered[names(go_all_markers_filtered) %in% goid_important]
-gfb_pred_important=gfb_pred[names(gfb_pred) %in% goid_important]
-
-snp_set_size=c(50,100,200,1000)
-random_gfb_pred=rep(list(list()),length(snp_set_size))
-names(random_gfb_pred)=names(snp_set_size)
-j=1
-for(s in snp_set_size)
-{
-	random_L2_2_gfblup_prediction_all=readRDS(file=gsub("[[:blank:]]", "", paste("/mnt/LTR_userdata/faroo002/arabidopsis/GP/GFBLUP/random_snp_sets/L2_2_gfblup_prediction_all_",s,".rds")))
-	no_of_repeats=length(random_L2_2_gfblup_prediction_all)
-	for(r in c(1:no_of_repeats))
-	{
-		if(length(random_L2_2_gfblup_prediction_all[[r]]$accuracy$Corr)>0)
-		{
-			random_gfb_pred[[j]]<-c(random_gfb_pred[[j]],as.list(random_L2_2_gfblup_prediction_all[[r]]$accuracy$Corr))
-		}
-	}
-	random_gf=na.omit(unlist(random_gfb_pred[[j]]))	
-j=j+1
-}
-boxplot(unlist(random_gfb_pred[[1]]),
-unlist(random_gfb_pred[[2]]),
-unlist(random_gfb_pred[[3]]),
-unlist(random_gfb_pred[[4]]),
-unlist(gfb_pred_important[[1]]),
-unlist(gfb_pred_important[[2]]),
-unlist(gfb_pred_important[[3]]),
-unlist(gfb_pred_important[[4]]),
-unlist(gfb_pred_important[[5]]),
-xlab="Gene ontology vs random SNP sampling",
-ylab="Predictive ability",
-names=c(snp_set_size,L2_2_all_important[,11]),
-main="Predictive ability using random SNP subsets vs GO based subsets")
-####################################################################################################################
diff --git a/code/using_GO/run_models.R b/code/using_GO/run_models.R
index 2b54de2..ed3786d 100644
--- a/code/using_GO/run_models.R
+++ b/code/using_GO/run_models.R
@@ -1,4 +1,23 @@
-cd /mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/
+##################################################################################################################################
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+setwd(paste0(wdir,"/",wd));
+##################################################################################################################################
+
 Rscript psii/H1_1_gblup_vs_gfblup_using_go_model_1_1000.R
 Rscript psii/H1_1_gblup_vs_gfblup_using_go_model_1001_2000.R
 Rscript psii/H1_1_gblup_vs_gfblup_using_go_model_2001_3000.R
@@ -483,4 +502,4 @@ Rscript pla/T20_2_4001_5000.R
 Rscript pla/T20_2_5001_6000.R
 Rscript pla/T20_2_6001_7297.R
 
-pla/8fold/combine.R
+Rscript pla/8fold/combine.R
diff --git a/code/using_GO/test.R b/code/using_GO/test.R
new file mode 100644
index 0000000..e00d397
--- /dev/null
+++ b/code/using_GO/test.R
@@ -0,0 +1,21 @@
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+if (rstudioapi::isAvailable()) {
+  if (require('rstudioapi') != TRUE) {
+    install.packages('rstudioapi')
+  }else{
+    library(rstudioapi) # load it
+  }
+ wdir <- dirname(getActiveDocumentContext()$path)
+}else{
+ wdir <- getwd()
+}
+this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())])
+if (length(this_file) > 0){
+  wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep)
+}else{
+  wd <- dirname(rstudioapi::getSourceEditorContext()$path)
+}
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+setwd(paste0(wdir,"/",wd));
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+print(getwd())
\ No newline at end of file
-- 
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