script: statistics~all-sample-combinations-DESeq2-edgeR "$scriptdir"/statistics~DESeq2 "$scriptdir"/statistics~edgeR
script: statistics~all-sample-combinations-DESeq2-edgeR "$scriptdir"/statistics~DESeq2 "$scriptdir"/statistics~edgeR "$scriptdir"/statistics~scatter_with_variance
c2997108/centos6:3 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 centos:centos6
using docker
+ set -o pipefail
+ p=0.05
+ sed 's/\r//g'
+ cat input_2/sample.input.txt
+ sed '/^$/d'
+ sed 's/ \+/\t/g; s/\t\+/\t/g; s/\t\+$//'
+ awk '-F\t' '{OFS="\t"; sub(/[.]gz$/,"",$1); print $0}'
+ awk '-F\t' '{gsub(/[^A-Za-z0-9._\t-]/,"_",$0); print $0}'
+ head -n 1 input_1/count.id.forDEGanalysis.txt
+ cut -f 2-
+ sed 's/\t/\n/g'
+ awk '-F\t' 'FILENAME==ARGV[1]{cat[$1]=$2} FILENAME==ARGV[2]{if(FNR==1){print "id\tcondition"}; if(cat[$1]==""){cat[$1]=$1}; print $1"\t"cat[$1]}' sample.txt2 /dev/stdin
+ '[' '!' -e isoforms.count_table ']'
+ ln -s input_1/count.id.forDEGanalysis.txt isoforms.count_table
+ tail -n+2 sample.input.txt
+ cut -f 2
+ sort -V
+ uniq
+ awk '{a[NR]=$1} END{for(i=1;i<=NR-1;i++){for(j=i+1;j<=NR;j++){print a[i]"\t"a[j]}}}'
+ cat
+ cat
+ countfile=isoforms.count_table
+ echo '
<h2>DEG analysis</h2>
 <h3>Differential expression analysis by DESeq2 with scatter plot of read counts (counts per million)</h3>
'
+ bash run-make-deg-html.sh isoforms.count_table DESeq2 0_result.html transcript
+ echo ' <h3>Differential expression analysis by edgeR with scatter plot of read counts (counts per million)</h3>'
+ bash run-make-deg-html.sh isoforms.count_table edgeR 0_result.html transcript
+ echo '</body></html>'
+ xargs -I '{}' -P 8 bash -c '{}'
+++ cat sample.input.pair.txt
+++ wc -l
++ seq 1 3
+ for i in '`seq 1 $(cat sample.input.pair.txt|wc -l)`'
++ head -n 1 sample.input.pair.txt
++ tail -n 1
++ cut -f 1
+ g1=Br
++ head -n 1 sample.input.pair.txt
++ tail -n 1
++ cut -f 2
+ g2=Fatbody
+ countfile=isoforms.count_table
+ '[' '' = '' ']'
+ awk '-F\t' '
   FILENAME==ARGV[1]{if(FNR>1){for(i=2;i<=NF;i++){a[i]+=$i}}}
   FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; for(i=2;i<=NF;i++){$i=$i" (CPM)"; if(a[i]==0){a[i]=1}}; print $0}
                     else{ORS=""; print $1;for(i=2;i<=NF;i++){print "\t"$i/a[i]*1000*1000}; print "\n"}}
  ' isoforms.count_table ./isoforms.count_table
+ annfile=isoforms.count_table.cpm
+ cat
+ docker run -v /data/user2/work/72:/data/user2/work/72 -w /data/user2/work/72 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 bash run-DE.Br.Fatbody.sh
+ awk '-F\t' -v g1=Br -v g2=Fatbody 'FILENAME==ARGV[1]{if(FNR==1){print $0}else{if($2==g1||$2==g2){print $0}}}' sample.input.txt
+ awk '-F\t' -v g1=Br '$2==g1{print $1}' sample.input.Br.Fatbody.txt
+ awk '-F\t' -v g2=Fatbody '$2==g2{print $1}' sample.input.Br.Fatbody.txt
+ awk '-F\t' -v g1=Br -v g2=Fatbody 'FILENAME==ARGV[1]{if($2==g1||$2==g2){flag[NR]=1}} FILENAME==ARGV[2]{ORS=""; print $1; for(i=2;i<=NF;i++){if(flag[i]==1){print "\t"$i}}; print "\n"}' sample.input.txt isoforms.count_table
+ echo N_SCRIPT=1 bash /data/user2/work/72/statistics~DESeq2 -s run-DESeq2.Br.Fatbody.isoform.R -i Br -j Fatbody -p 0.05 isoforms.count_table.Br.Fatbody.txt sample.input.Br.Fatbody.txt '\'\''isoforms.count_table.cpm\'\''' '> log-DESeq2.Br.Fatbody.isoform.txt 2>&1'
+ echo N_SCRIPT=1 bash /data/user2/work/72/statistics~edgeR -s run-edgeR.Br.Fatbody.isoform.R -i Br -j Fatbody -p 0.05 isoforms.count_table.Br.Fatbody.txt sample.input.Br.Fatbody.txt '\'\''isoforms.count_table.cpm\'\''' '> log-edgeR.Br.Fatbody.isoform.txt 2>&1'
+ for i in '`seq 1 $(cat sample.input.pair.txt|wc -l)`'
++ head -n 2 sample.input.pair.txt
++ tail -n 1
++ cut -f 1
+ g1=Br
++ head -n 2 sample.input.pair.txt
++ tail -n 1
++ cut -f 2
+ g2=Germ
+ countfile=isoforms.count_table
+ '[' '' = '' ']'
+ awk '-F\t' '
   FILENAME==ARGV[1]{if(FNR>1){for(i=2;i<=NF;i++){a[i]+=$i}}}
   FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; for(i=2;i<=NF;i++){$i=$i" (CPM)"; if(a[i]==0){a[i]=1}}; print $0}
                     else{ORS=""; print $1;for(i=2;i<=NF;i++){print "\t"$i/a[i]*1000*1000}; print "\n"}}
  ' isoforms.count_table ./isoforms.count_table
+ annfile=isoforms.count_table.cpm
+ cat
+ docker run -v /data/user2/work/72:/data/user2/work/72 -w /data/user2/work/72 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 bash run-DE.Br.Germ.sh
+ awk '-F\t' -v g1=Br -v g2=Germ 'FILENAME==ARGV[1]{if(FNR==1){print $0}else{if($2==g1||$2==g2){print $0}}}' sample.input.txt
+ awk '-F\t' -v g1=Br '$2==g1{print $1}' sample.input.Br.Germ.txt
+ awk '-F\t' -v g2=Germ '$2==g2{print $1}' sample.input.Br.Germ.txt
+ awk '-F\t' -v g1=Br -v g2=Germ 'FILENAME==ARGV[1]{if($2==g1||$2==g2){flag[NR]=1}} FILENAME==ARGV[2]{ORS=""; print $1; for(i=2;i<=NF;i++){if(flag[i]==1){print "\t"$i}}; print "\n"}' sample.input.txt isoforms.count_table
+ echo N_SCRIPT=1 bash /data/user2/work/72/statistics~DESeq2 -s run-DESeq2.Br.Germ.isoform.R -i Br -j Germ -p 0.05 isoforms.count_table.Br.Germ.txt sample.input.Br.Germ.txt '\'\''isoforms.count_table.cpm\'\''' '> log-DESeq2.Br.Germ.isoform.txt 2>&1'
+ echo N_SCRIPT=1 bash /data/user2/work/72/statistics~edgeR -s run-edgeR.Br.Germ.isoform.R -i Br -j Germ -p 0.05 isoforms.count_table.Br.Germ.txt sample.input.Br.Germ.txt '\'\''isoforms.count_table.cpm\'\''' '> log-edgeR.Br.Germ.isoform.txt 2>&1'
+ for i in '`seq 1 $(cat sample.input.pair.txt|wc -l)`'
++ head -n 3 sample.input.pair.txt
++ tail -n 1
++ cut -f 1
+ g1=Fatbody
++ head -n 3 sample.input.pair.txt
++ tail -n 1
++ cut -f 2
+ g2=Germ
+ countfile=isoforms.count_table
+ '[' '' = '' ']'
+ awk '-F\t' '
   FILENAME==ARGV[1]{if(FNR>1){for(i=2;i<=NF;i++){a[i]+=$i}}}
   FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; for(i=2;i<=NF;i++){$i=$i" (CPM)"; if(a[i]==0){a[i]=1}}; print $0}
                     else{ORS=""; print $1;for(i=2;i<=NF;i++){print "\t"$i/a[i]*1000*1000}; print "\n"}}
  ' isoforms.count_table ./isoforms.count_table
+ annfile=isoforms.count_table.cpm
+ cat
+ docker run -v /data/user2/work/72:/data/user2/work/72 -w /data/user2/work/72 -u root -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 bash run-DE.Fatbody.Germ.sh
+ awk '-F\t' -v g1=Fatbody -v g2=Germ 'FILENAME==ARGV[1]{if(FNR==1){print $0}else{if($2==g1||$2==g2){print $0}}}' sample.input.txt
+ awk '-F\t' -v g1=Fatbody '$2==g1{print $1}' sample.input.Fatbody.Germ.txt
+ awk '-F\t' -v g2=Germ '$2==g2{print $1}' sample.input.Fatbody.Germ.txt
+ awk '-F\t' -v g1=Fatbody -v g2=Germ 'FILENAME==ARGV[1]{if($2==g1||$2==g2){flag[NR]=1}} FILENAME==ARGV[2]{ORS=""; print $1; for(i=2;i<=NF;i++){if(flag[i]==1){print "\t"$i}}; print "\n"}' sample.input.txt isoforms.count_table
+ echo N_SCRIPT=1 bash /data/user2/work/72/statistics~DESeq2 -s run-DESeq2.Fatbody.Germ.isoform.R -i Fatbody -j Germ -p 0.05 isoforms.count_table.Fatbody.Germ.txt sample.input.Fatbody.Germ.txt '\'\''isoforms.count_table.cpm\'\''' '> log-DESeq2.Fatbody.Germ.isoform.txt 2>&1'
+ echo N_SCRIPT=1 bash /data/user2/work/72/statistics~edgeR -s run-edgeR.Fatbody.Germ.isoform.R -i Fatbody -j Germ -p 0.05 isoforms.count_table.Fatbody.Germ.txt sample.input.Fatbody.Germ.txt '\'\''isoforms.count_table.cpm\'\''' '> log-edgeR.Fatbody.Germ.isoform.txt 2>&1'
+ post_processing
+ '[' 1 = 1 ']'
+ '[' 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']'
+ docker run -v /data/user2/work/72:/data/user2/work/72 -w /data/user2/work/72 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit