Commit 9b2ca054 authored by Aflitos, Saulo Alves's avatar Aflitos, Saulo Alves
Browse files

bug fix

parent c4347ffc
......@@ -6,3 +6,4 @@
*.dot
*.png
*.html
*.out
#!/bin/bash
set -xeu
LOGFILE="SConstruct.run.log."`date +%Y%m%d_%H%M%S`".out"
#echo "LOGFILE $LOGFILE"
python scons/scons.py -n --stack-size=1024 --diskcheck=none $@ 2>&1 | tee $LOGFILE
......@@ -4,7 +4,7 @@ rm SConstruct.tree.png 2>/dev/null
rm SConstruct.tree.gif 2>/dev/null
rm SConstruct.tree.html 2>/dev/null
bash SConstruct.run -n --tree=prune,status $@ > SConstruct.tree.dat
bash SConstruct.run -n --tree=prune,status $@ | grep -v '+-/' > SConstruct.tree.dat
#,derived
cat SConstruct.tree.dat | python SConstruct.graph.py $@
......
#in fasta in csv
sa1/sa.fa sa1/sa.csv
#sa2/sa.fa sa2/sa.csv
sh1/sh.fa sh1/sh.csv
#sh2/sh.fa sh2/sh.csv
#sl1/sl.fa sl1/sl.csv
#sl2/sl.fa sl2/sl.csv
sp1/sp.fa sp1/sp.csv
#sp2/sp.fa sp2/sp.csv
This diff is collapsed.
#group name platform library name library size library size min library size max file names
120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79 illumina pe 500 450 550 /home/assembly/tomato150/reseq/raw/074/illumina/pairedend_500/120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/raw/074/illumina/pairedend_500/120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79_2.fq.gz.clean.dup.clean.gz
120524_I238_FCD1174ACXX_L4_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L4_SZAXPI009266-140_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120524_I238_FCD1174ACXX_L4_SZAXPI009266-140_1.fq.gz.clean.dup.clean.gz
120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140_2.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L1_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCD117YACXX_L1_SZAXPI009266-140_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/pairedend_170/120530_I235_FCD117YACXX_L1_SZAXPI009266-140_1.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/raw/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
20000.dedup 454 mp 20000 18000 22000 /home/assembly/tomato150/denovo/pennellii/filtered/454/20000/20000.dedup.sff
8000.dedup 454 mp 8000 7200 8800 /home/assembly/tomato150/denovo/pennellii/filtered/454/8000/8000.dedup.sff
120524_I238_FCD1174ACXX_L4_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L4_SZAXPI009266-140_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L4_SZAXPI009266-140_1.fq.gz.clean.dup.clean.gz
120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L4_SZAXPI009266-140_2.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L1_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/filtered/illumina/pairedend_170/120530_I235_FCD117YACXX_L1_SZAXPI009266-140_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/pairedend_170/120530_I235_FCD117YACXX_L1_SZAXPI009266-140_1.fq.gz.clean.dup.clean.gz
120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79 illumina pe 500 450 550 /home/assembly/tomato150/reseq/filtered/074/illumina/pairedend_500/120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/filtered/074/illumina/pairedend_500/120512_I238_FCC0U42ACXX_L1_SZAXPI008753-79_2.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
20000.dedup 454 mp 20000 18000 22000 /home/assembly/tomato150/denovo/pennellii/filtered/454/20000/20000.dedup.sff
8000.dedup 454 mp 8000 7200 8800 /home/assembly/tomato150/denovo/pennellii/filtered/454/8000/8000.dedup.sff
3000.dedup 454 mp 3000 2700 3300 /home/assembly/tomato150/denovo/pennellii/filtered/454/3000/3000.dedup.sff
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