diff --git a/.gitignore b/.gitignore
index 87b9045e5ea387a3bbff850d38b2908e17066524..968fe90e6bdcbccf2a94b29a262eef1ee6cec906 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,9 @@
 *.png
 *.html
 *.out
+*/db
+*/in
+*/output
+*/map
+*.fa
+scons/
diff --git a/all3.csv b/all3.csv
index ac83f39e0192a82c28e0e0be366862504219a012..f414e6d8f6155d128d4511c7283c86a98077575c 100644
--- a/all3.csv
+++ b/all3.csv
@@ -1,16 +1,16 @@
 #in fasta	in csv
-#sa1/sa.fa	sa1/sa.csv
-#sa2/sa.fa	sa2/sa.csv
-sa3/sa.fa	sa3/sa.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
-sh3/sh.fa	sh3/sh.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
+sl1/sl.fa	sl1/sl.csv
 
-#sp1/sp.fa	sp1/sp.csv
-#sp2/sp.fa	sp2/sp.csv
+sp1/sp.fa	sp1/sp.csv
+sp2/sp.fa	sp2/sp.csv
 sp3/sp.fa	sp3/sp.csv
 
+heinz/heinz.fa	heinz/heinz.csv
+pimp/heinz.fa	pimp/pimp.csv
+
diff --git a/heinz/heinz.csv b/heinz/heinz.csv
new file mode 100644
index 0000000000000000000000000000000000000000..d3da803946c908f494ce5c3fefaf9e3c308a53ba
--- /dev/null
+++ b/heinz/heinz.csv
@@ -0,0 +1,24 @@
+#group name	platform	library name	library size	library size min	library size max	file names
+30507AAXX_6	illumina	pe	160	144	176	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/30507AAXX_6_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/30507AAXX_6_f.fastq
+30507AAXX_7	illumina	pe	160	144	176	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/30507AAXX_7_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/30507AAXX_7_f.fastq
+30507AAXX_8	illumina	pe	160	144	176	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/30507AAXX_8_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/30507AAXX_8_f.fastq
+314TYAAXX_1	illumina	pe	160	144	176	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/314TYAAXX_1_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/314TYAAXX_1_r.fastq
+314TYAAXX_2	illumina	pe	160	144	176	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/314TYAAXX_2_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/314TYAAXX_2_r.fastq
+314TYAAXX_3	illumina	pe	160	144	176	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/314TYAAXX_3_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/314TYAAXX_3_r.fastq
+314TYAAXX_4	illumina	pe	160	144	176	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/314TYAAXX_4_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_250/314TYAAXX_4_r.fastq
+30507AAXX_1	illumina	pe	215	193	237	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/30507AAXX_1_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/30507AAXX_1_f.fastq
+30507AAXX_2	illumina	pe	215	193	237	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/30507AAXX_2_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/30507AAXX_2_f.fastq
+30507AAXX_3	illumina	pe	215	193	237	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/30507AAXX_3_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/30507AAXX_3_f.fastq
+30507AAXX_4	illumina	pe	215	193	237	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/30507AAXX_4_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/30507AAXX_4_f.fastq
+314TYAAXX_6	illumina	pe	215	193	237	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/314TYAAXX_6_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/314TYAAXX_6_r.fastq
+314TYAAXX_7	illumina	pe	215	193	237	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/314TYAAXX_7_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/314TYAAXX_7_r.fastq
+314TYAAXX_8	illumina	pe	215	193	237	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/314TYAAXX_8_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_300/314TYAAXX_8_r.fastq
+#sample_R	illumina	pe	500	450	550	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_500/sample_R1_001.64.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/Heinz_Illumina_pairedend_500/sample_R2_001.64.fastq
+#3018DAAXX_1	illumina	mp	1640	1440	1840	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_2000/3018DAAXX_1_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_2000/3018DAAXX_1_f.fastq
+#3018DAAXX_2	illumina	mp	2430	2180	2680	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_3000/3018DAAXX_2_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_3000/3018DAAXX_2_r.fastq
+#3018DAAXX_3	illumina	mp	2850	2550	3150	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_4000/3018DAAXX_3_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_4000/3018DAAXX_3_f.fastq
+#3018DAAXX_4	illumina	mp	3000	2500	3500	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_5000/3018DAAXX_4_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_5000/3018DAAXX_4_f.fastq
+#30THBAAXX_1	illumina	mp	1640	1440	1840	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_2000/30THBAAXX_1_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_2000/30THBAAXX_1_r.fastq
+#30THBAAXX_2	illumina	mp	2430	2180	2680	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_3000/30THBAAXX_2_r.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_3000/30THBAAXX_2_f.fastq
+#30THBAAXX_3	illumina	mp	2850	2550	3150	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_4000/30THBAAXX_3_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_4000/30THBAAXX_3_r.fastq
+#30THBAAXX_4	illumina	mp	3000	2500	3500	/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_5000/30THBAAXX_4_f.fastq;/home/assembly/tomato150/dev150/assemblies/mapping/heinz/in/MP_5000/30THBAAXX_4_r.fastq
diff --git a/heinz/mean_coverage.pl b/heinz/mean_coverage.pl
new file mode 100644
index 0000000000000000000000000000000000000000..c6ff42ebc4aacdcde1b56f87efc0932c2384b919
--- /dev/null
+++ b/heinz/mean_coverage.pl
@@ -0,0 +1,30 @@
+($num,$den,$min,$max,$av,$var)=(0,0,10000000,0,0,0);
+while ($cov=<STDIN>) {
+    if ( $cov >= 1 ) {
+        $num += $cov;
+        if ( $cov > $max ) { $max = $cov; };
+        if ( $cov < $min ) { $min = $cov; };
+        if ( $den == 0   ) { $av=$cov; $var=0; }
+        else {
+                $av   = (($av*$den)+$cov)/($den+1);
+                $var += ($cov-$av)**2;
+                $dev  = sqrt($var/$den);
+		if ( $den % 10000 == 0 ) {
+                	print "$den\t$av\t$var\t$dev\n";
+		}
+        };
+        $den++;
+    }
+}
+$cov=$num/$den;
+$dev=sqrt($var/$den);
+$mx=$cov+(2*$dev);
+print "Length        = $den\n";
+print "Bases         = $num\n";
+print "Mean Coverage = $cov\n";
+print "Min  Coverage = $min\n";
+print "Max  Coverage = $max\n";
+print "Var  Coverage = $var\n";
+print "Dev  Coverage = $dev\n";
+print "MX   Coverage = $mx\n";
+
diff --git a/heinz/run.sh b/heinz/run.sh
new file mode 100644
index 0000000000000000000000000000000000000000..632e186364f892e182d4fb9114fffa849c569f73
--- /dev/null
+++ b/heinz/run.sh
@@ -0,0 +1 @@
+./SConstruct.run --incsv=all3.csv --threads=10 -j 5 heinz
diff --git a/heinz/snpcalling.txt b/heinz/snpcalling.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62b2b91f2a0eecd2679c28c6e4dab0d0b725aea1
--- /dev/null
+++ b/heinz/snpcalling.txt
@@ -0,0 +1,121 @@
+#http://samtools.sourceforge.net/mpileup.shtml
+
+For variant calling by Samtools, we used following commands.
+ 
+samtools calmd | samtools mpileup | bcftools view: to create raw variant bcf files
+Options "-AEur" used for calmd.
+generates extra tags (MD tags) with high sensitivity (-Ar), capping it (I dont know what it means) and exporting as uncompresse (-u) bam.
+ 
+Options "-d 99999 -L 99999 -Dugf" were used for mpileup.
+For each position read at most 99999 reads (-d), dont skip indels (-L 99999),  output per sample read depth (-D), export as uncompressed BCF (-ug) 
+ 
+Options "-bvcg" were used for view.
+ output as BCF (-b) showing only variant sites (-vc) for each sample (-g) 
+ 
+ 
+vcfutils.pl varFilter: to filter and create variant vcf files
+Options "-W 5 -Q 20 -d 4 -D xxx" were used. Upper depth (-D) of each sample was set based on depth distribution of the sample.
+Filter adjacent gaps with a window size of 5 (-W)  minimum RMS quality of 20 (-Q, i dont know what it means), minimum depth of 4 (-d) and a custom maximum depth depending on the actual depth (i guess average)
+
+/usr/share/samtools/vcfutils.pl
+
+
+
+
+INBAM1=output/heinz.fa.bam.filtered.bam
+RUNNAME=output/heinz.fa.bam.filtered.bam
+REF=heinz.fa
+
+
+samtools rmdup $INBAM1 $RUNNAME.dedup.bam
+samtools calmd -AEur $RUNNAME.dedup.bam $REF | samtools mpileup -d 99999 -L 99999 -Dugf $REF - | bcftools view -bvcg - > $RUNNAME.dedup.bam.bcf
+bcftools view $RUNNAME.dedup.bam.bcf         | /usr/share/samtools/vcfutils.pl varFilter -W 5 -Q 20 -d 4 -D100 > $RUNNAME.dedup.bam.bcf.vcf
+
+
+samtools mpileup $RUNNAME.dedup.bam | awk '{print $4}' | perl mean_coverage.pl
+cat output/heinz.fa.bam.filtered.bam.dedup.bam.bcf.vcf | grep -v \# | cut -f 8 | cut -d ';' -f 1 | grep -v INDEL | cut -d '=' -f 2 | perl -ne 'BEGIN{$v=0;$c=0;$min=10000000;$max=0;$av=0;$var=0;} END{ $a=$v/$c; $dev=sqrt($var/$c); $mx=$a+(2*$dev); print "$c\t$v\t$a\t$min\t$max\t$av\t$var\t$dev\t$mx\n"; } $c+=1; $v+=$_; if ($_ < $min) { $min = $_; }; if ($_ > $max) { $max = $_; }; if ($c==1) { $av = $_; $var=0; } else { $av=(($av*$c)+$_)/($c+1); $var+=($_-$av)**2; $dev=sqrt($var/$c); print "$av\t$var\t$dev\n";}'
+
+heinz dedup : BAM : Length        =       725,678,368
+heinz dedup : BAM : Bases         =    15,270,968,181
+heinz dedup : BAM : Mean Coverage =                21.04
+heinz dedup : BAM : Min  Coverage =                 1
+heinz dedup : BAM : Max  Coverage =             8,010
+heinz dedup : BAM : Var  Coverage =   934,577,172,304.24
+heinz dedup : BAM : Dev  Coverage =                35.89
+heinz dedup : BAM : MX   Coverage =                92.82
+
+heinz dedup : VCF : POSITION      =           370,742
+heinz dedup : VCF : SUM COV       =         7,425,739
+heinz dedup : VCF : AVG COV       =                20.03
+heinz dedup : VCF : MIN COV       =                 4
+heinz dedup : VCF : MAX COV       =               100
+heinz dedup : VCF : VAR COV       =        75,974,225.29
+heinz dedup : VCF : STDDEV COV    =                14.31
+heinz dedup : VCF : 2DEV COV      =                48.66
+
+RF_001      : BAM : Length        =       733,900,334
+RF_001      : BAM : Bases         =    28,464,215,562
+RF_001      : BAM : Mean Coverage =                38.78
+RF_001      : BAM : Min  Coverage =                 1
+RF_001      : BAM : Max  Coverage =             7,861
+RF_001      : BAM : Var  Coverage = 1,355,682,620,730.03
+RF_001      : BAM : Dev  Coverage =                42.98
+RF_001      : BAM : MX   Coverage =               124.74
+
+RF_001      : VCF : POSITION      =           237,532
+RF_001      : VCF : SUM COV       =        10,093,075
+RF_001      : VCF : AVG COV       =                42.49
+RF_001      : VCF : MIN COV       =                 4
+RF_001      : VCF : MAX COV       =               105
+RF_001      : VCF : VAR COV       =        97,797,311.67
+RF_001      : VCF : STDDEV COV    =                20.29
+RF_001      : VCF : 2DEV COV      =                82.58
+
+
+samtools mpileup ~/tomato150/Disk02_bam_ass_nobackup/reseq/mapped/Heinz/RF_001_SZAXPI008746-45.bam | awk '{print $4}' | perl mean_coverage.pl | tee RF_001.bam.cov_stats
+gunzip -c ~/tomato150/programs/snpeff/newest/datain/RF_001_SZAXPI008746-45.vcf.gz | grep -v \# | cut -f 8 | cut -d ';' -f 1 | grep -v INDEL | cut -d '=' -f 2 | perl -ne 'BEGIN{$v=0;$c=0;$min=10000000;$max=0;$av=0;$var=0;} END{ $a=$v/$c; $dev=sqrt($var/$c); $mx=$a+(2*$dev); print "$c\t$v\t$a\t$min\t$max\t$av\t$var\t$dev\t$mx\n"; } $c+=1; $v+=$_; if ($_ < $min) { $min = $_; }; if ($_ > $max) { $max = $_; }; if ($c==1) { $av = $_; $var=0; } else { $av=(($av*$c)+$_)/($c+1); $var+=($_-$av)**2; $dev=sqrt($var/$c); print "$av\t$var\t$dev\n";}'
+
+
+
+wc -l *.vcf
+  410.804 heinz.fa.bam.filtered.bam.dedup.bam.bcf.vcf
+  200.015 heinz.fa.bam.filtered.bam.dedup.bam.bcf.vcf.qual20.vcf
+  610.819 total
+
+
+
+=========================================================================================
+($num,$den,$min,$max,$av,$var)=(0,0,10000000,0,0,0);
+while ($cov=<STDIN>) {
+    if ( $cov >= 1 ) {
+	$c   += 1;
+        $num += $cov;
+        if ( $cov > $max ) { $max = $cov; };
+        if ( $cov < $min ) { $min = $cov; };
+	if ( $c == 0     ) { $av=$cov; $var=0; }
+	else { 
+		$av   = (($av*$den)+$cov)/($den+1); 
+		$var += ($cov-$av)**2; 
+		$dev  = sqrt($var/$den); 
+                if ( $den % 10000 == 0 ) {
+                        print "$den\t$av\t$var\t$dev\n";
+                }
+	};
+        $den++;
+    }
+}
+$cov=$num/$den;
+$dev=sqrt($var/$c); 
+$mx=$cov+(2*$dev);
+print "Length        = $den\n";
+print "Bases         = $num\n";
+print "Mean Coverage = $cov\n";
+print "Min  Coverage = $min\n";
+print "Max  Coverage = $max\n";
+print "Var  Coverage = $var\n";
+print "Dev  Coverage = $dev\n";
+print "MX   Coverage = $mx\n";
+
+
+
+
diff --git a/pimp/in/mkreport.sh b/pimp/in/mkreport.sh
new file mode 100755
index 0000000000000000000000000000000000000000..6f24d1f5974bd8c049fe46397a762223361ba5a5
--- /dev/null
+++ b/pimp/in/mkreport.sh
@@ -0,0 +1,69 @@
+#!/bin/bash
+
+set -xeu
+
+WID=800
+HEI=600
+NUM=9
+
+
+F1=$1
+F2=$2
+
+
+if [[ ! -f "white.png" ]]; then
+	convert -size ${WID}x${HEI} xc:white white.png
+fi
+
+function do_report {
+    reportfolderOut=$1
+    reportfolder=${reportfolderOut}_fastqc
+
+    if [[ ! -f "$reportfolder/Images/kmer_profiles.png" ]]; then
+        #kmer_profiles.png
+        cp white.png $reportfolder/Images/kmer_profiles.png
+    fi
+
+    images=`find $reportfolder/Images -type f -name '*.png' | sort | tr '\n' ' '`
+    #echo "    IMAGES $images"
+    IMC=`find $reportfolder/Images -type f -name '*.png' | wc -l`
+
+    if [[ "$IMC" -ne "$NUM" ]]; then
+        echo "wrong number of images $IMC (should be $NUM)"
+        exit 1
+    fi
+
+    if [[ -f "$reportfolderOut.png" ]]; then
+        #rm $reportfolder.png
+        echo -n
+    fi
+
+    WIDT=$(($WID*1   ))
+    HEIT=$(($HEI*$NUM))
+    CMD="montage -verbose -label '%f' -font Helvetica  -pointsize 14 -background 'white' -fill 'black' -define png:size=${WIDT}x${HEIT} -geometry ${WID}x${HEI}+2+2 -tile 1x$NUM -auto-orient $images $reportfolderOut.png"
+    echo $CMD
+    eval $CMD
+}
+
+
+N1=${F1%%.*}
+N2=${F2%%.*}
+
+O1=$N1.png
+O2=$N2.png
+
+do_report $N1
+do_report $N2
+
+
+LCN=`python -c "import os,sys; print os.path.commonprefix([sys.argv[1], sys.argv[2]])" $N1 $N2`.png
+LCN=`basename $LCN`
+WIDT=$(($WID*2   ))
+HEIT=$(($HEI*$NUM))
+
+CMD="montage -verbose -label '%f' -font Helvetica  -pointsize 14 -background 'white' -fill 'black' -define png:size=${WIDT}x${HEIT} -geometry ${WID}x${HEIT}+2+2 -tile 2x1 -auto-orient $O1 $O2 $LCN"
+echo "     LCN $LCN"
+echo "     width        $WID  height       $HEI  num $NUM images 2"
+echo "     width total  $WIDT height total $HEIT"
+#echo "     CMD $CMD"
+eval $CMD
diff --git a/pimp/mean_coverage.pl b/pimp/mean_coverage.pl
new file mode 120000
index 0000000000000000000000000000000000000000..306ab2e243556f446bcd2b0a34996722ccddcc1c
--- /dev/null
+++ b/pimp/mean_coverage.pl
@@ -0,0 +1 @@
+../heinz/mean_coverage.pl
\ No newline at end of file
diff --git a/pimp/pimp.csv b/pimp/pimp.csv
new file mode 100644
index 0000000000000000000000000000000000000000..2629fb6e1709e889b4e3786099a0959ade58c7b5
--- /dev/null
+++ b/pimp/pimp.csv
@@ -0,0 +1,2 @@
+#group name	platform	library name	library size	library size min	library size max	file names
+C3VVEACXX	illumina	pe	160	144	176	/home/assembly/tomato150/dev150/assemblies/mapping/pimp/in/pimpinellifolium_NoIndex_L003_R1_001.fastq.gz;/home/assembly/tomato150/dev150/assemblies/mapping/pimp/in/pimpinellifolium_NoIndex_L003_R2_001.fastq.gz
diff --git a/pimp/run.sh b/pimp/run.sh
new file mode 100644
index 0000000000000000000000000000000000000000..f03253ff53356b88a0a4838bfb0447b61afd6c4d
--- /dev/null
+++ b/pimp/run.sh
@@ -0,0 +1 @@
+./SConstruct.run --incsv=all3.csv --threads=10 -j 5 pimp
diff --git a/pimp/snp.sh b/pimp/snp.sh
new file mode 100644
index 0000000000000000000000000000000000000000..38e0cca934a5e589fc2cd2963ec5528d1109eb82
--- /dev/null
+++ b/pimp/snp.sh
@@ -0,0 +1,27 @@
+INBAM1=/home/assembly/tomato150/dev150/assemblies/mapping/pimp/output/C3VVEACXX.bam.filtered.bam
+RUNNAME=/home/assembly/tomato150/dev150/assemblies/mapping/pimp/output/C3VVEACXX.bam.filtered.bam
+REF=heinz.fa
+
+
+samtools rmdup $INBAM1 $RUNNAME.dedup.bam
+samtools calmd -AEur   $RUNNAME.dedup.bam $REF | samtools mpileup -d 99999 -L 99999 -Dugf $REF - | bcftools view -bvcg - > $RUNNAME.dedup.bam.bcf
+bcftools view          $RUNNAME.dedup.bam.bcf  | /usr/share/samtools/vcfutils.pl varFilter -W 5 -Q 20 -d 4 -D100         > $RUNNAME.dedup.bam.bcf.vcf
+
+
+samtools mpileup $RUNNAME.dedup.bam | awk '{print $4}' | perl mean_coverage.pl
+
+cat $RUNNAME.dedup.bam.bcf.vcf | \
+	grep -v \# | \
+	cut -f 8 | \
+	cut -d ';' -f 1 | \
+	grep -v INDEL | \
+	cut -d '=' -f 2 | \
+	perl -ne 'BEGIN{$v=0;$c=0;$min=10000000;$max=0;$av=0;$var=0;} END{ $a=$v/$c; $dev=sqrt($var/$c); $mx=$a+(2*$dev); print "$c\t$v\t$a\t$min\t$max\t$av\t$var\t$dev\t$mx\n"; } $c+=1; $v+=$_; if ($_ < $min) { $min = $_; }; if ($_ > $max) { $max = $_; }; if ($c==1) { $av = $_; $var=0; } else { $av=(($av*$c)+$_)/($c+1); $var+=($_-$av)**2; $dev=sqrt($var/$c); print "$av\t$var\t$dev\n";}' | \
+	tee $RUNNAME.dedup.bam.bcf.vcf.stats
+
+
+samtools index    $RUNNAME.dedup.bam
+samtools depth    $RUNNAME.dedup.bam > $RUNNAME.dedup.bam.cov
+samtools idxstats $RUNNAME.dedup.bam > $RUNNAME.dedup.bam.idxflags
+samtools flagstat $RUNNAME.dedup.bam > $RUNNAME.dedup.bam.stats
+
diff --git a/pimp/snpcalling.txt b/pimp/snpcalling.txt
new file mode 120000
index 0000000000000000000000000000000000000000..a25eb1917e49b89b44f184d54c41146a781a0c30
--- /dev/null
+++ b/pimp/snpcalling.txt
@@ -0,0 +1 @@
+../heinz/snpcalling.txt
\ No newline at end of file
diff --git a/run2.py b/run2.py
index 302f37726aef70422dbccfb229a4315a90187fb1..08dd184d68f901f032ca116b62d2031631357ea0 100755
--- a/run2.py
+++ b/run2.py
@@ -9,6 +9,8 @@ import glob
 import atexit
 from pprint import pprint as pp
 
+#./SConstruct.runReal --incsv=all3.csv --threads=20 -j 5 all
+
 dry_run      = False
 #dry_run      = True
 
@@ -255,7 +257,7 @@ def addCommand(name, cmd, TARGET=None, SOURCE=[], DATA={}, DEPS=[], REQS=[], PRE
                     valStr         = " ".join([str(x) for x in val])
                     valindex       = data.index(val)
                     data[valindex] = valStr
-                    print "  CONVERTING %s FROM %s TO %s" % (key, val, valStr)
+                    print "  CONVERTING FROM %s TO %s" % (val, valStr)
 
 
     #print "checking target"
@@ -462,13 +464,13 @@ def main():
                     os.makedirs(out_folder)
 
             projsetup = {
-                'proj_name'  : proj_name,
-                'in_fasta'   : in_fasta,
-                'in_csv'     : in_csv,
-                'base_folder': base_folder,
-                'db_folder'  : db_folder,
-                'map_folder' : map_folder,
-                'out_folder' : out_folder
+                    'proj_name'  : proj_name,
+                    'in_fasta'   : in_fasta,
+                    'in_csv'     : in_csv,
+                    'base_folder': base_folder,
+                    'db_folder'  : db_folder,
+                    'map_folder' : map_folder,
+                    'out_folder' : out_folder
                 }
             pp(projsetup)
             setup.append(projsetup)
@@ -488,8 +490,8 @@ def main():
         print "target %s: %s" % (projsetup['proj_name'].upper(), projsetup['outfile'])
     print "\n\n\n"
 
-def project( setup ):
 
+def project( setup ):
     datas   = {}
 
     ##########################
@@ -608,10 +610,10 @@ def process454(data, setup):
 
         out_fastq   = out_prefix + '.fastq'
 
+        out_fastq_0 = out_fastq.replace('.fastq', '_0.fastq')
         out_fastq_f = out_fastq.replace('.fastq', '_1.fastq')
         out_fastq_r = out_fastq.replace('.fastq', '_2.fastq')
         out_fastq_n = out_fastq.replace('.fastq', '_n.fastq')
-        out_fastq_0 = out_fastq.replace('.fastq', '_0.fastq')
 
         data[comm_name]['file_names'      ] = [out_fastq_f, out_fastq_r]
         data[comm_name]['file_names_454'  ] = infile
@@ -758,16 +760,22 @@ def run_bwa(data, setup):
         CMD_MAPPER1  = "%(bwa_exe)s aln -t %(threads)d %(db_name)s %(fastq1cmd)s > %(TARGET)s"
         CMD_MAPPER2  = "%(bwa_exe)s aln -t %(threads)d %(db_name)s %(fastq2cmd)s > %(TARGET)s"
 
-        CMD_ALIGNER  = "%(bwa_exe)s sampe -o 20 -P -f %(TARGET)s "
+        CMD_ALIGNER  = "%(bwa_exe)s sampe -o 20 -P "
+        #CMD_ALIGNER  = "%(bwa_exe)s sampe -o 20 -P -f %(TARGET)s "
+
         if 'gsize' in info:
             CMD_ALIGNER  += " -a %(gmax)s "
         CMD_ALIGNER += "%(db_name)s %(sai1)s %(sai2)s %(fastq1cmd)s %(fastq2cmd)s"
 
-        CMD_CONVERT  = "%(samtools_exe)s view -S -b -q 30 -1 %(sam)s > %(TARGET)s" # TARGET = bam_tmp
+        CMD_ALIGNER += " | %(samtools_exe)s view -Su -b -q 30 -1 -"
+        #CMD_CONVERT  = "%(samtools_exe)s view -S -b -q 30 -1 %(sam)s > %(TARGET)s" # TARGET = bam_tmp
         #CMD_MV1      = "mv %(bam_tmp_rnd)s %(bam_tmp)s"
-        CMD_SORT     = "%(samtools_exe)s sort -m 53687091200 -o -l 1 -@ 20 -m 2G %(bam_tmp)s %(TARGET)s > %(TARGET)s"
+
+        CMD_ALIGNER += " | %(samtools_exe)s sort -m 53687091200 -o -l 1 -@ 20 -m 2G - %(TARGET)s > %(TARGET)s"
+        #CMD_SORT     = "%(samtools_exe)s sort -m 53687091200 -o -l 1 -@ 20 -m 2G %(bam_tmp)s %(TARGET)s > %(TARGET)s"
         #samtools sort -m 53687091200 -o -l 1 -@ 20 -m 2G 136.bam /run/shm/bwa_scons_mapping_13117_J9DFw5 > /run/shm/bwa_scons_mapping_13117_J9DFw5
         #CMD_MV2      = "mv %(bam_pfx_rnd_bam)s %(bam)s"
+
         CMD_INDEX    = '%(samtools_exe)s index    %(bam)s'
         CMD_COV      = '%(samtools_exe)s depth    %(bam)s   > %(TARGET)s'
         CMD_STATS    = '%(samtools_exe)s idxstats %(bam)s   > %(TARGET)s'
@@ -777,19 +785,21 @@ def run_bwa(data, setup):
 
         addCommand('map'             , CMD_MAPPER1, TARGET = info['sai1']              , SOURCE = info['fastq1']                                           , DATA = info, REQS = [ info['bwt_index'] ]                    , USETMP=True )
         addCommand('map'             , CMD_MAPPER2, TARGET = info['sai2']              , SOURCE = info['fastq2']                                           , DATA = info, REQS = [ info['bwt_index'] ]                    , USETMP=True )
-        addCommand('align'           , CMD_ALIGNER, TARGET = info['sam']               , SOURCE = [ info['fastq1'], info['fastq2'] ]                       , DATA = info, DEPS = [ bwt_index, info['sai1'], info['sai2'] ], USETMP=True )
+        #addCommand('align'           , CMD_ALIGNER, TARGET = info['sam']               , SOURCE = [ info['fastq1'], info['fastq2'] ]                       , DATA = info, DEPS = [ bwt_index, info['sai1'], info['sai2'] ], USETMP=True )
+        addCommand('align'           , CMD_ALIGNER, TARGET = info['bam']               , SOURCE = [ info['fastq1'], info['fastq2'] ]                       , DATA = info, DEPS = [ bwt_index, info['sai1'], info['sai2'] ], USETMP=True )
+
 
         CMD_CONVERT_tmp = False
         if (not os.path.exists(info['bam'])) or ( os.path.getsize(info['bam']) == 0 ):
             CMD_CONVERT_tmp = True
-        addCommand('convert'         , CMD_CONVERT, TARGET = info['bam_tmp']           , SOURCE = info['sam'        ]                                      , DATA = info                                                   , USETMP=True )
+        #addCommand('convert'         , CMD_CONVERT, TARGET = info['bam_tmp']           , SOURCE = info['sam'        ]                                      , DATA = info                                                   , USETMP=True )
         #addCommand('moving'         , CMD_MV1    , TARGET = info['bam_tmp'    ]       , SOURCE = info['bam_tmp_rnd']                                      , DATA = info)
 
 
-        CMD_SORT_tmp = False
-        if (not os.path.exists(info['bam'])) or ( os.path.getsize(info['bam']) == 0 ):
-            CMD_SORT_tmp = True
-        addCommand('sort'            , CMD_SORT   , TARGET = info['bam']                , SOURCE = info['bam_tmp'    ]                                      , DATA = info                                                  , USETMP=True)
+        #CMD_SORT_tmp = False
+        #if (not os.path.exists(info['bam'])) or ( os.path.getsize(info['bam']) == 0 ):
+        #    CMD_SORT_tmp = True
+        #addCommand('sort'            , CMD_SORT   , TARGET = info['bam']                , SOURCE = info['bam_tmp'    ]                                      , DATA = info                                                  , USETMP=True)
         #addCommand('moving'          , move       , TARGET = info['bam']               , SOURCE = info['bam_pfx_rnd_bam']                                  , DATA = info)
 
         addCommand('index'           , CMD_INDEX  , TARGET = info['bai']               , SOURCE = info['bam']                                              , DATA = info                                                                )
@@ -825,29 +835,30 @@ def run_bwa(data, setup):
     addCommand('preoking'            , CMD_PRE_OK , TARGET = pre_ok                , SOURCE = oks, DATA = data )
 
 
-    ##########################
-    ## IF NOT TO MERGE, STOPS HERE
-    ##########################
-    setup['data'] = data
-    if not do_merge:
-        print "FINISHED", setup['proj_name']
-        env.Alias( setup['proj_name'], pre_ok )
-        setup['bamdata'] = ""
-        setup['outfile'] = pre_ok
-        return [ pre_ok ]
+    RND_NAME1 = None
+    RND_NAME2 = None
+    bam_tmp   = '%s.tmp.bam' % bam_name
+    bam_sht   = '%s'         % bam_name
+    bam_out   = '%s.bam'     % bam_name
 
+    if ( not do_merge ) or ( len(bams) == 1 ):
+        bam_name  = bams[0]
+        RND_NAME1 = ""
+        RND_NAME2 = ""
+        bam_tmp   = '%s.tmp.bam' % bam_name
+        bam_sht   = '%s'         % bam_name
+        bam_out   = '%s'         % bam_name
+
+    else:
+        RND_NAME1 = tempfile.mktemp(dir=TMP_FOLDER, prefix='bwa_', suffix='.bam')
+        RND_NAME2 = tempfile.mktemp(dir=TMP_FOLDER, prefix='bwa_', suffix='.bam')
+        bam_tmp   = '%s.tmp.bam' % bam_name
+        bam_sht   = '%s'         % bam_name
+        bam_out   = '%s.bam'     % bam_name
 
 
 
-    ##########################
-    ## MERGE BAMS
-    ##########################
-    bam_tmp  = '%s.tmp.bam' % bam_name
-    bam_sht  = '%s'         % bam_name
-    bam_out  = '%s.bam'     % bam_name
 
-    RND_NAME1 = tempfile.mktemp(dir=TMP_FOLDER, prefix='bwa_', suffix='.bam')
-    RND_NAME2 = tempfile.mktemp(dir=TMP_FOLDER, prefix='bwa_', suffix='.bam')
 
     bam_data = {
         'samtools_exe': SAMTOOLS_EXE,
@@ -864,6 +875,7 @@ def run_bwa(data, setup):
         'stat'        : bam_out   + '.stats',
         'bok'         : bam_out   + '.ok',
         'flag'        : bam_out   + '.flagstats',
+
         'filter'      : bam_out   + '.filtered.bam',
         #'fix'         : bam_out   + '.filtered.bam.fixmate.bam',
         #'dedup'       : bam_out   + '.filtered.bam.dedup.bam',
@@ -872,6 +884,16 @@ def run_bwa(data, setup):
         'fstat'       : bam_out   + '.filtered.bam.stats',
         'fflag'       : bam_out   + '.filtered.bam.flagstats',
         'fok'         : bam_out   + '.filtered.bam.ok',
+
+        'dedup'       : bam_out   + '.filtered.bam.dedup.bam',
+        #'fix'         : bam_out   + '.filtered.bam.fixmate.bam',
+        #'dedup'       : bam_out   + '.filtered.bam.dedup.bam',
+        'dindex'      : bam_out   + '.filtered.bam.dedup.bam.bai',
+        'dcov'        : bam_out   + '.filtered.bam.dedup.bam.cov',
+        'dstat'       : bam_out   + '.filtered.bam.dedup.bam.stats',
+        'dflag'       : bam_out   + '.filtered.bam.dedup.bam.flagstats',
+        'dok'         : bam_out   + '.filtered.bam.dedup.bam.ok',
+
         'bams'        : " ".join(bams)
     }
 
@@ -896,6 +918,26 @@ def run_bwa(data, setup):
 
 
 
+    ##########################
+    ## IF NOT TO MERGE, STOPS HERE
+    ##########################
+    setup['data'] = data
+    if ( not do_merge ) or ( len(bams) == 1 ):
+        bam_data['bok'] = info['ok']
+
+        filterbam(bam_data)
+
+        print "FINISHED", setup['proj_name']
+        env.Alias( setup['proj_name'], bam_data['dok'] )
+        setup['bamdata'] = bam_data
+        setup['outfile'] = bam_data['dok']
+        return [ bam_data['dok'] ]
+
+
+
+    ##########################
+    ## MERGE BAMS
+    ##########################
     # attatch RG tag (source), min compression
     CMD_MERGE  = '%(samtools_exe)s merge -r -1         %(TARGET)s %(bams)s'
     #CMD_MV1    = "mv %(bamrnd1)s %(bam)s"
@@ -904,15 +946,6 @@ def run_bwa(data, setup):
     CMD_STAT   = '%(samtools_exe)s idxstats            %(bam)s    > %(TARGET)s'
     CMD_FLAG   = '%(samtools_exe)s flagstat            %(bam)s    > %(TARGET)s'
     CMD_BOK    = touch
-    CMD_FILTER = '%(samtools_exe)s view %(sam_filter)s -b %(bam)s > %(TARGET)s'
-    #CMD_MV2    = 'mv %(bamrnd2)s %(filter)s'
-    #CMD_FIX    = '%(samtools_exe)s fixmate             %(filter)s %(fix)s'
-    #CMD_DEDUP  = '%(samtools_exe)s rmdup -S            %(filter)s %(dedup)s'
-    CMD_FINDEX = '%(samtools_exe)s index               %(filter)s'
-    CMD_FCOV   = '%(samtools_exe)s depth               %(filter)s > %(TARGET)s'
-    CMD_FSTAT  = '%(samtools_exe)s idxstats            %(filter)s > %(TARGET)s'
-    CMD_FFLAG  = '%(samtools_exe)s flagstat            %(filter)s > %(TARGET)s'
-    CMD_FOK    = touch
 
 
     CMD_MERGE_tmp = False
@@ -930,6 +963,26 @@ def run_bwa(data, setup):
     bdeps = [ bam_data['index'], bam_data['cov'], bam_data['stat'], bam_data['flag'] ]
     addCommand('bam ok'         , CMD_BOK   , TARGET = bam_data['bok']    , SOURCE = bdeps                                                               )
 
+    filterbam(bam_data)
+
+    if __name__ == 'SCons.Script':
+        print "FINISHED", setup['proj_name']
+        env.Alias( setup['proj_name'], bam_data['dok'] )
+        setup['bamdata'] = bam_data
+        setup['outfile'] = bam_data['dok']
+        return [ bam_data['dok'] ]
+
+def filterbam( bam_data ):
+    CMD_FILTER = '%(samtools_exe)s view %(sam_filter)s -b %(bam)s > %(TARGET)s'
+    #CMD_MV2    = 'mv %(bamrnd2)s %(filter)s'
+    #CMD_FIX    = '%(samtools_exe)s fixmate             %(filter)s %(fix)s'
+    #CMD_DEDUP  = '%(samtools_exe)s rmdup -S            %(filter)s %(dedup)s'
+    CMD_FINDEX = '%(samtools_exe)s index               %(filter)s'
+    CMD_FCOV   = '%(samtools_exe)s depth               %(filter)s > %(TARGET)s'
+    CMD_FSTAT  = '%(samtools_exe)s idxstats            %(filter)s > %(TARGET)s'
+    CMD_FFLAG  = '%(samtools_exe)s flagstat            %(filter)s > %(TARGET)s'
+    CMD_FOK    = touch
+
     CMD_FILTER_tmp = False
     if ( not os.path.exists( bam_data['filter'] )) or ( os.path.getsize(bam_data['filter']) == 0 ):
         CMD_FILTER_tmp = True
@@ -951,13 +1004,35 @@ def run_bwa(data, setup):
                                                                                     ]                   , DATA = bam_data                                )
 
 
-    if __name__ == 'SCons.Script':
-        print "FINISHED", setup['proj_name']
-        env.Alias( setup['proj_name'], bam_data['fok'] )
-        setup['bamdata'] = bam_data
-        setup['outfile'] = bam_data['fok']
-        return [ bam_data['fok'] ]
+    CMD_DEDUP  = '%(samtools_exe)s rmdup               %(filter)s   %(TARGET)s'
+    #CMD_MV2    = 'mv %(bamrnd2)s %(filter)s'
+    #CMD_FIX    = '%(samtools_exe)s fixmate             %(filter)s %(fix)s'
+    #CMD_DEDUP  = '%(samtools_exe)s rmdup -S            %(filter)s %(dedup)s'
+    CMD_DINDEX = '%(samtools_exe)s index               %(filter)s'
+    CMD_DCOV   = '%(samtools_exe)s depth               %(filter)s > %(TARGET)s'
+    CMD_DSTAT  = '%(samtools_exe)s idxstats            %(filter)s > %(TARGET)s'
+    CMD_DFLAG  = '%(samtools_exe)s flagstat            %(filter)s > %(TARGET)s'
+    CMD_DOK    = touch
+
+    CMD_DEDUP_tmp = False
+    if ( not os.path.exists( bam_data['dedup'] )) or ( os.path.getsize(bam_data['dedup']) == 0 ):
+        CMD_DEDUP_tmp = True
 
+    addCommand('deduping'       , CMD_DEDUP , TARGET = bam_data['dedup']  , SOURCE = bam_data['filter'] , DATA = bam_data, DEPS = [ bam_data['fok']    ], USETMP=CMD_DEDUP_tmp )
+    #addCommand('moving'        , CMD_MV2   , TARGET = bam_data['filter'] , SOURCE = bam_data['bamrnd2'], DATA = bam_data                                )
+
+
+    addCommand('Dindexing'      , CMD_DINDEX, TARGET = bam_data['dindex'] , SOURCE = bam_data['dedup']  , DATA = bam_data                                             )
+    addCommand('Dcoverage'      , CMD_DCOV  , TARGET = bam_data['dcov']   , SOURCE = bam_data['dedup']  , DATA = bam_data, DEPS = [ bam_data['dindex'] ], USETMP=True )
+    addCommand('Dstatistics'    , CMD_DSTAT , TARGET = bam_data['dstat']  , SOURCE = bam_data['dedup']  , DATA = bam_data, DEPS = [ bam_data['dindex'] ], USETMP=True )
+    addCommand('Dflag stats'    , CMD_DFLAG , TARGET = bam_data['dflag']  , SOURCE = bam_data['dedup']  , DATA = bam_data, DEPS = [ bam_data['dindex'] ], USETMP=True )
+    addCommand('Dok'            , CMD_DOK   , TARGET = bam_data['dok']    , SOURCE = [
+                                                                                    bam_data['dindex' ],
+                                                                                    bam_data['dcov'   ],
+                                                                                    bam_data['dstat'  ],
+                                                                                    bam_data['dflag'  ],
+                                                                                    bam_data['fok']
+                                                                                    ]                   , DATA = bam_data                                )
 
 
 def bf_to_str(bf):
diff --git a/sa1/sa.csv b/sa1/sa.csv
index d23dc9ff3277dfd259c8e8aa7eb3866b69f72d36..295472f899632462202552d2a9264cc5915cd2c6 100644
--- a/sa1/sa.csv
+++ b/sa1/sa.csv
@@ -1,12 +1,12 @@
 #group name	platform	library name	library size	library size min	library size max	file names
-120524_I238_FCD1174ACXX_L2_SZAXPI009264-133	illumina	pe	170	153	187	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L2_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L2_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz
-120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133	illumina	pe	170	153	187	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz
-120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133	illumina	pe	170	153	187	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz
+120524_I238_FCD1174ACXX_L2_SZAXPI009264-133	illumina	pe	170	153	187	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L2_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L2_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz
+120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133	illumina	pe	170	153	187	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120527_I247_FCC0U0NACXX_L6_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz
+120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133	illumina	pe	170	153	187	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009264-133_2.fq.gz.clean.dup.clean.gz
 120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46	illumina	pe	500	450	550	/home/assembly/tomato150/reseq/filtered/058/illumina/pairedend_500/120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/filtered/058/illumina/pairedend_500/120530_I649_FCC0U6WACXX_L4_SZAXPI009359-46_2.fq.gz.clean.dup.clean.gz
 120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93	illumina	mp	2000	1800	2200	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz
 120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93	illumina	mp	2000	1800	2200	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120530_I235_FCC0U06ACXX_L1_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz
-120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93	illumina	mp	2000	1800	2200	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz
-120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93	illumina	mp	2000	1800	2200	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz
+120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93	illumina	mp	2000	1800	2200	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120615_I248_FCD14ADACXX_L7_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz
+120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93	illumina	mp	2000	1800	2200	/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/arcanum/filtered/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L5_TOMxitDGJDWAAPEI-93_2.fq.gz.clean.dup.clean.gz
 20000.dedup	454	mp	20000	18000	22000	/home/assembly/tomato150/denovo/arcanum/filtered/454/20000/20000.dedup.sff
 8000.dedup	454	mp	8000	7200	8800	/home/assembly/tomato150/denovo/arcanum/filtered/454/8000/8000.dedup.sff
 
diff --git a/sa1/sa.groups.csv b/sa1/sa.groups.csv
deleted file mode 120000
index 44be302312b82f8bb30236e770e6e20e7f9b4510..0000000000000000000000000000000000000000
--- a/sa1/sa.groups.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_sample_arcanum_raw/in_groups2.csv
\ No newline at end of file
diff --git a/sa1/sa.libs.csv b/sa1/sa.libs.csv
deleted file mode 120000
index dba8698185d5c22f5a8a61bb55f0a0520ffa7484..0000000000000000000000000000000000000000
--- a/sa1/sa.libs.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_sample_arcanum_raw/in_libs2.csv
\ No newline at end of file
diff --git a/sa2/run.py b/sa2/run.py
deleted file mode 120000
index b2af2326060ab4d54b535a1beba01ad0228427e8..0000000000000000000000000000000000000000
--- a/sa2/run.py
+++ /dev/null
@@ -1 +0,0 @@
-../run.py
\ No newline at end of file
diff --git a/sa2/sa.fa b/sa2/sa.fa
index 756e5ce87476ea222287411c43b5e4301925990f..28265c306598cf333d80f3fb2b370cbc42191502 120000
--- a/sa2/sa.fa
+++ b/sa2/sa.fa
@@ -1 +1 @@
-../../allpaths_lg_sample_arcanum_raw/sa/data/run/ASSEMBLIES/test2/final.assembly.fasta
\ No newline at end of file
+../../allpaths_lg_sample_arcanum_raw/sa/data/run/ASSEMBLIES/test2/final.contigs.fasta
\ No newline at end of file
diff --git a/sa2/sa.groups.csv b/sa2/sa.groups.csv
deleted file mode 120000
index 44be302312b82f8bb30236e770e6e20e7f9b4510..0000000000000000000000000000000000000000
--- a/sa2/sa.groups.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_sample_arcanum_raw/in_groups2.csv
\ No newline at end of file
diff --git a/sa2/sa.libs.csv b/sa2/sa.libs.csv
deleted file mode 120000
index dba8698185d5c22f5a8a61bb55f0a0520ffa7484..0000000000000000000000000000000000000000
--- a/sa2/sa.libs.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_sample_arcanum_raw/in_libs2.csv
\ No newline at end of file
diff --git a/sh1/sh.csv b/sh1/sh.csv
index 81a3c10ec628a2f15890e720c4b971721b173cd9..f3e73d4583abeaf853f757b3053c316e88aac2a3 100644
--- a/sh1/sh.csv
+++ b/sh1/sh.csv
@@ -2,10 +2,10 @@
 120524_I238_FCD1174ACXX_L3_SZAXPI009265-136	illumina	pe	170	153	187	/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L3_SZAXPI009265-136_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L3_SZAXPI009265-136_2.fq.gz.clean.dup.clean.gz
 120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136	illumina	pe	170	153	187	/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120530_I235_FCC0U06ACXX_L8_SZAXPI009265-136_2.fq.gz.clean.dup.clean.gz
 120530_I235_FCD117YACXX_L7_SZAXPI009265-136	illumina	pe	170	153	187	/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120530_I235_FCD117YACXX_L7_SZAXPI009265-136_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/pairedend_170/120530_I235_FCD117YACXX_L7_SZAXPI009265-136_2.fq.gz.clean.dup.clean.gz
-120512_I238_FCD115HACXX_L1_SZAXPI008752-75	illumina	pe	500	450	550	/home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120512_I238_FCD115HACXX_L1_SZAXPI008752-75_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120512_I238_FCD115HACXX_L1_SZAXPI008752-75_1.fq.gz.clean.dup.clean.gz
-120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75	illumina	pe	500	450	550	/home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75_1.fq.gz.clean.dup.clean.gz
+120512_I238_FCD115HACXX_L1_SZAXPI008752-75	illumina	pe	500	450	550	/home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120512_I238_FCD115HACXX_L1_SZAXPI008752-75_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120512_I238_FCD115HACXX_L1_SZAXPI008752-75_2.fq.gz.clean.dup.clean.gz
+120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75	illumina	pe	500	450	550	/home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/reseq/filtered/072/illumina/pairedend_500/120613_I246_FCC0WM1ACXX_L7_SZAXPI008752-75_2.fq.gz.clean.dup.clean.gz
 120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90	illumina	mp	2000	1800	2200	/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120524_I238_FCD1174ACXX_L7_TOMxitDGKDWAAPEI-90_2.fq.gz.clean.dup.clean.gz
 120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90	illumina	mp	2000	1800	2200	/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L7_TOMxitDGKDWAAPEI-90_2.fq.gz.clean.dup.clean.gz
-120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90	illumina	mp	2000	1800	2200	/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90_1.fq.gz.clean.dup.clean.gz
+120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90	illumina	mp	2000	1800	2200	/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/habrochaites/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGKDWAAPEI-90_2.fq.gz.clean.dup.clean.gz
 20000.dedup	454	mp	20000	18000	22000	/home/assembly/tomato150/denovo/habrochaites/filtered/454/20000/20000.dedup.sff
 8000.dedup	454	mp	8000	7200	8800	/home/assembly/tomato150/denovo/habrochaites/filtered/454/8000/8000.dedup.sff
diff --git a/sh1/sh.groups.csv b/sh1/sh.groups.csv
deleted file mode 120000
index 78bb6a49bbed9363443b4178b957dd215eb50eaf..0000000000000000000000000000000000000000
--- a/sh1/sh.groups.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_habrochaites_raw/in_groups.csv
\ No newline at end of file
diff --git a/sh1/sh.libs.csv b/sh1/sh.libs.csv
deleted file mode 120000
index 3376ea01c874b1843660c511c338168cd16c7c93..0000000000000000000000000000000000000000
--- a/sh1/sh.libs.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_habrochaites_raw/in_libs.csv
\ No newline at end of file
diff --git a/sh2/sh.fa b/sh2/sh.fa
index 5e6914cc0f71faa2563618a424638a0c91f76e3a..870d516e2c7c2dd1679d8d03e093cc2516589ce8 120000
--- a/sh2/sh.fa
+++ b/sh2/sh.fa
@@ -1 +1 @@
-../../allpaths_lg_habrochaites_raw/sh/data/run/ASSEMBLIES/test2/final.assembly.fasta
\ No newline at end of file
+../../allpaths_lg_habrochaites_raw/sh/data/run/ASSEMBLIES/test2/final.contigs.fasta
\ No newline at end of file
diff --git a/sh2/sh.groups.csv b/sh2/sh.groups.csv
deleted file mode 120000
index 78bb6a49bbed9363443b4178b957dd215eb50eaf..0000000000000000000000000000000000000000
--- a/sh2/sh.groups.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_habrochaites_raw/in_groups.csv
\ No newline at end of file
diff --git a/sl1/run.py b/sl1/run.py
deleted file mode 120000
index b2af2326060ab4d54b535a1beba01ad0228427e8..0000000000000000000000000000000000000000
--- a/sl1/run.py
+++ /dev/null
@@ -1 +0,0 @@
-../run.py
\ No newline at end of file
diff --git a/sl1/sl.fa b/sl1/sl.fa
index e91afcfcb27dece25aeed564c55d0a48a55f710d..713a313b68c05f526423341746a7102d32e7bbf9 120000
--- a/sl1/sl.fa
+++ b/sl1/sl.fa
@@ -1 +1 @@
-../../allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
\ No newline at end of file
+../../allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.contigs.fasta
\ No newline at end of file
diff --git a/sl1/sl.groups.csv b/sl1/sl.groups.csv
deleted file mode 120000
index bcbf57e362bbc7ae32c34ef39e47d1bbbff2c1a7..0000000000000000000000000000000000000000
--- a/sl1/sl.groups.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_sample_heinz_raw/in_groups_heinz.csv
\ No newline at end of file
diff --git a/sl1/sl.libs.csv b/sl1/sl.libs.csv
deleted file mode 120000
index af27025951551d9feb21b4d6e40458128678806f..0000000000000000000000000000000000000000
--- a/sl1/sl.libs.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_sample_heinz_raw/in_libs_heinz.csv
\ No newline at end of file
diff --git a/sp1/run.py b/sp1/run.py
deleted file mode 120000
index b2af2326060ab4d54b535a1beba01ad0228427e8..0000000000000000000000000000000000000000
--- a/sp1/run.py
+++ /dev/null
@@ -1 +0,0 @@
-../run.py
\ No newline at end of file
diff --git a/sp1/sp.csv b/sp1/sp.csv
index f1dacf430d315280df1e55810be903e76f9fdfd3..bb7c546e9881bd0b8692cd211c280214f5e14b14 100644
--- a/sp1/sp.csv
+++ b/sp1/sp.csv
@@ -1,13 +1,13 @@
 #group name	platform	library name	library size	library size min	library size max	file names
-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
+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_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/pairedend_170/120524_I238_FCD1174ACXX_L4_SZAXPI009266-140_2.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
+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_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/pairedend_170/120530_I235_FCD117YACXX_L1_SZAXPI009266-140_2.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
+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_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_2.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
+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_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_2.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_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/filtered/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_2.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
diff --git a/sp1/sp.groups.csv b/sp1/sp.groups.csv
deleted file mode 120000
index 092a6fdfeba79fa70aaa5d987d37c21fae192808..0000000000000000000000000000000000000000
--- a/sp1/sp.groups.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_pennellii_raw/in_groups2.csv
\ No newline at end of file
diff --git a/sp1/sp.libs.csv b/sp1/sp.libs.csv
deleted file mode 120000
index 945ecca20e6aaae2c5299be8966c2aea4a6bb359..0000000000000000000000000000000000000000
--- a/sp1/sp.libs.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_pennellii_raw/in_libs2.csv
\ No newline at end of file
diff --git a/sp2/sp.groups.csv b/sp2/sp.groups.csv
deleted file mode 120000
index 092a6fdfeba79fa70aaa5d987d37c21fae192808..0000000000000000000000000000000000000000
--- a/sp2/sp.groups.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_pennellii_raw/in_groups2.csv
\ No newline at end of file
diff --git a/sp2/sp.libs.csv b/sp2/sp.libs.csv
deleted file mode 120000
index 945ecca20e6aaae2c5299be8966c2aea4a6bb359..0000000000000000000000000000000000000000
--- a/sp2/sp.libs.csv
+++ /dev/null
@@ -1 +0,0 @@
-../../allpaths_lg_pennellii_raw/in_libs2.csv
\ No newline at end of file