pp statistics~edgeR -c 8 -m 32 input_1/fin.qiu.genes.count_table input_2/Qiu.fin2.txt Checking the realpath of input files. 0 input_1/fin.qiu.genes.count_table 0 input_2/Qiu.fin2.txt 0 /home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work /home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev /home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR /data/yoshitake.kazutoshi/work /data/yoshitake.kazutoshi/work/pp-dev /data/yoshitake.kazutoshi/work/pp-dev/yoshitake /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR script: /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/statistics~edgeR "$scriptdir"/statistics~scatter_with_variance c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 centos:centos6 using docker + set -o pipefail + script=run-edgeR.R + inputmatrix=input_1/fin.qiu.genes.count_table + inputmatrix=input_1/fin.qiu.genes.count_table + sed '/^$/d' + cat input_2/Qiu.fin2.txt + sed 's/ \+/\t/g; s/\t\+/\t/g; s/\t\+$//; s/[.]gz\t/\t/' + awk '-F\t' '{gsub(/[^A-Za-z0-9._\t-]/,"_",$0); print $0}' + sed 's/\r//g' ++ basename input_1/fin.qiu.genes.count_table ++ basename input_1/fin.qiu.genes.count_table + inputsamplematrix=input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt + g1= + g2= + '[' '' = '' ']' ++ tail -n+2 input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt ++ sort -V ++ uniq ++ head -n 1 ++ cut -f 2 + g1=female_long + '[' '' = '' ']' ++ uniq ++ sort -V ++ cut -f 2 ++ tail -n 1 ++ tail -n+2 input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt ++ head -n 2 + g2=female_short + p=0.05 ++ basename input_1/fin.qiu.genes.count_table + outputfile=edgeR.fin.qiu.genes.count_table ++ basename input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt ++ basename input_1/fin.qiu.genes.count_table + samplex=edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.x ++ basename input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt ++ basename input_1/fin.qiu.genes.count_table + sampley=edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.y ++ basename input_1/fin.qiu.genes.count_table + outputfilexup=result.edgeR.fin.qiu.genes.count_table.female_long.up.female_short.down.txt ++ basename input_1/fin.qiu.genes.count_table + outputfileyup=result.edgeR.fin.qiu.genes.count_table.female_long.down.female_short.up.txt + '[' '' = '' ']' + annotationfile=input_1/fin.qiu.genes.count_table ++ awk '-F\t' -v g1=female_long -v g2=female_short 'FILENAME==ARGV[1]{gp[$1]=$2} FILENAME==ARGV[2] && FNR==1{ORS=""; for(i=2;i<=NF;i++){if(gp[$i]==g1){print "1,"}else if(gp[$i]==g2){print "2,"}else{print "3,"}}}' input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt input_1/fin.qiu.genes.count_table ++ sed 's/,$//' + gp=3,3,3,3,2,3,1,3,3,3,3,2,3,3,3,2,2,3,3,3,3,3,3,3,2,3,3,3,3,2,3,3,2,3,3,3,3,3,3,3,3,3 + cat + FUNC_RUN_DOCKER c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 R --vanilla + PP_RUN_IMAGE=c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 + shift + PP_RUN_DOCKER_CMD=("${@}") ++ date +%Y%m%d_%H%M%S_%3N + PPDOCNAME=pp20230907_180800_836_14074 + echo pp20230907_180800_836_14074 ++ id -u ++ id -g + docker run --name pp20230907_180800_836_14074 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -u 2007:600 -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 R --vanilla R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(edgeR) Loading required package: limma > x <- round(read.table("input_1/fin.qiu.genes.count_table",sep="\t",header=T,row.names=1)) > group <- factor(c(3,3,3,3,2,3,1,3,3,3,3,2,3,3,3,2,2,3,3,3,3,3,3,3,2,3,3,3,3,2,3,3,2,3,3,3,3,3,3,3,3,3)) > y <- DGEList(counts=x,group=group) > y <- calcNormFactors(y) > design <- model.matrix(~group) > y <- estimateDisp(y,design) > fit <- glmQLFit(y,design) > qlf <- glmQLFTest(fit,coef=2) > res=topTags(qlf,n=dim(x)[1]) > res=res[res$table$FDR<0.05,] > write.table(as.data.frame(res),file="edgeR.fin.qiu.genes.count_table",quote=F,sep="\t") > + '[' '!' -e edgeR.fin.qiu.genes.count_table ']' + awk '-F\t' 'NR>1{print $1}' edgeR.fin.qiu.genes.count_table + awk '-F\t' -v g1=female_long '$2==g1{print $1}' input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt + awk '-F\t' -v g2=female_short '$2==g2{print $1}' input_2/Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt + bash /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/statistics~scatter_with_variance -x female_long -y female_short input_1/fin.qiu.genes.count_table edgeR.fin.qiu.genes.count_table.id edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.x edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.y Checking the realpath of input files. 0 input_1/fin.qiu.genes.count_table 0 edgeR.fin.qiu.genes.count_table.id 0 edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.x 0 edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.y c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 centos:centos6 using docker + set -o pipefail + countmat=input_1/fin.qiu.genes.count_table + sigmat=edgeR.fin.qiu.genes.count_table.id + listx=edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.x + listy=edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.y + label_x=female_long + label_y=female_short + p=0.05 ++ basename input_1/fin.qiu.genes.count_table ++ basename edgeR.fin.qiu.genes.count_table.id + output=fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id + cat input_1/fin.qiu.genes.count_table + awk '-F\t' 'FILENAME==ARGV[1]{if(FNR>1){for(i=2;i<=NF;i++){a[i]+=$i}}} FILENAME==ARGV[2]{if(FNR==1){print $0}else{ORS=""; print $1;for(i=2;i<=NF;i++){print "\t"$i/a[i]*1000*1000}; print "\n"}}' /dev/stdin input_1/fin.qiu.genes.count_table + cat edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.x + awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=1} FILENAME==ARGV[2]{if(FNR==1){for(i=1;i<=NF;i++){if(a[$i]==1){b[i]=1}}}; ORS=""; print $1; for(i=2;i<=NF;i++){if(b[i]==1){print "\t"$i}}; print "\n"}' /dev/stdin fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm + cat edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.y + awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=1} FILENAME==ARGV[2]{if(FNR==1){for(i=1;i<=NF;i++){if(a[$i]==1){b[i]=1}}}; ORS=""; print $1; for(i=2;i<=NF;i++){if(b[i]==1){print "\t"$i}}; print "\n"}' /dev/stdin fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm + cat edgeR.fin.qiu.genes.count_table.id + awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=1} FILENAME==ARGV[2] && (FNR==1 || a[$1]==1){print $0}' /dev/stdin fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm_x + cat edgeR.fin.qiu.genes.count_table.id + awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=1} FILENAME==ARGV[2] && (FNR==1 || a[$1]==1){print $0}' /dev/stdin fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm_y + cat + FUNC_RUN_DOCKER c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 R --vanilla + PP_RUN_IMAGE=c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 + shift + PP_RUN_DOCKER_CMD=("${@}") ++ date +%Y%m%d_%H%M%S_%3N + PPDOCNAME=pp20230907_180837_948_18482 + echo pp20230907_180837_948_18482 ++ id -u ++ id -g + docker run --name pp20230907_180837_948_18482 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -u 2007:600 -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 R --vanilla R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > label_x="female_long" > label_y="female_short" > file_data_x="fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm_x" > file_data_y="fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm_y" > file_sig_data_x="fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm_x_sig" > file_sig_data_y="fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm_y_sig" > data_x=round(read.table(file_data_x,sep="\t",header=T,row.names=1)) > data_y=round(read.table(file_data_y,sep="\t",header=T,row.names=1)) > sig_data_x=read.table(file_sig_data_x,sep="\t",header=T,row.names=1) > if(dim(sig_data_x)[1]!=0){sig_data_x=round(sig_data_x)} > sig_data_y=read.table(file_sig_data_y,sep="\t",header=T,row.names=1) > if(dim(sig_data_y)[1]!=0){sig_data_y=round(sig_data_y)} > mean_data_x=apply(data_x,1,mean) > mean_data_y=apply(data_y,1,mean) > if(dim(data_x)[2]>1){ + dx=apply(data_x,1,function(i){return(abs(qt(0.05/2, length(i)-1)) * sd(i) / sqrt(length(i)))}) + }else{ + dx=0 + } > if(dim(data_y)[2]>1){ + dy=apply(data_y,1,function(i){return(abs(qt(0.05/2, length(i)-1)) * sd(i) / sqrt(length(i)))}) + }else{ + dy=0 + } > vx=dx/mean_data_x > vy=dy/mean_data_y > vx[is.na(vx)]=0 > vy[is.na(vy)]=0 > #total_var_data=sqrt(dx^2+dy^2)/sqrt(mean_data_x^2+mean_data_y^2) > #total_var_data[is.na(total_var_data)]=0 > total_var_data=sqrt(vx^2+vy^2) > mean_sig_data_x=apply(sig_data_x,1,mean) > mean_sig_data_y=apply(sig_data_y,1,mean) > min_x=min(mean_data_x[mean_data_x>0])/10 > min_y=min(mean_data_y[mean_data_y>0])/10 > plot_mean_data_x=mean_data_x+min_x > plot_mean_data_y=mean_data_y+min_y > plot_mean_sig_data_x=mean_sig_data_x+min_x > plot_mean_sig_data_y=mean_sig_data_y+min_y > max_x=max(plot_mean_data_x) > max_y=max(plot_mean_data_y) > library(Cairo) > mainplotfunc=function(){ + if(max(dx,dy)>0){ + start_class=quantile(total_var_data[total_var_data>0],c(0,1,25,50,75,90,100)/100)[2] + end_class=quantile(total_var_data[total_var_data>0],c(0,1,25,50,75,90,100)/100)[6] + + CairoPNG("fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.scatter.png",width=800,height=600) + num_class=22 + library(RColorBrewer) + #mycol=colorRampPalette(c(rgb(0.5,0,0.2,0.4),rgb(1,0.8,0.7,1)), alpha=TRUE)(num_class) + colPal3 <- colorRampPalette(brewer.pal(9,"YlOrRd")[3:9]) + mycol=colPal3(num_class) + + layout(matrix(c(1,1,1,1,2),1,5)) + par(ps = 18) + k=0 + i=end_class + n=(total_var_data>=i) + xt=plot_mean_data_x[n] + yt=plot_mean_data_y[n] + plot(xt,yt,log="xy",xlim=c(min_x,max_x),ylim=c(min_y,max_y),cex=2*(k+1)^3/num_class^3,pch=21,col=adjustcolor(mycol[k+1],0),bg=adjustcolor(mycol[k+1],1-0.4*k/num_class),xlab=label_x,ylab=label_y) + + for(k in 1:(num_class-2)){ + i=end_class+(start_class-end_class)*k/(num_class-2) + n=(total_var_data>=i & total_var_data=i & total_var_data=",i),pos=4) + } + k=num_class-1 + i=min(total_var_data) + par(new=T) + plot(c(0),c(k),xlim=c(0,0),ylim=c(-1,num_class),col=adjustcolor(mycol[k+1],0),bg=adjustcolor(mycol[k+1],1-0.4*k/num_class),pch=21,cex=2*(k+1)^3/num_class^3,bty="n",axes=F,xlab="",ylab="") + text(c(0.05),c(k),paste(">=",i),pos=4) + text(0,num_class+0.2,"95%conf/mean") + par(new=T) + plot(c(-0.3),c(-1),xlim=c(0,0),ylim=c(-1,num_class),col="green",cex=1,bty="n",axes=F,xlab="",ylab="") + text(c(-0.3),c(-1),paste("significant"),pos=4) + + dev.off() + } + } > subplotfunc=function(){ + CairoPNG("fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.scatter.normal.png",width=600,height=600) + plot(plot_mean_data_x,plot_mean_data_y,log="xy",xlim=c(min_x,max_x),ylim=c(min_y,max_y),cex=0.1,pch=21,col=adjustcolor("#000000",0.5),xlab=label_x,ylab=label_y) + par(new=T) + plot(plot_mean_sig_data_x,plot_mean_sig_data_y,log="xy",xlim=c(min_x,max_x),ylim=c(min_y,max_y),col="green",cex=2,axes=F,xlab="",ylab="") + dev.off() + } > > wflag=0 > while(wflag<=5){ + restry=NULL + restry=try(mainplotfunc(), silent = FALSE) + if(class(restry)!="try-error"){break} + try(dev.off()) + Sys.sleep(10+runif(1, min=0,max=100)/10) + wflag=wflag+1 + } > wflag=0 > while(wflag<=5){ + restry=NULL + restry=try(subplotfunc(), silent = FALSE) + if(class(restry)!="try-error"){break} + try(dev.off()) + Sys.sleep(10+runif(1, min=0,max=100)/10) + wflag=wflag+1 + } > > > + rm -f fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm_x fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm_y fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm_x_sig fin.qiu.genes.count_table.edgeR.fin.qiu.genes.count_table.id.cpm_y_sig + post_processing + '[' 2 = 1 ']' + exit + awk '{if($2<=0){print $1"\tx"}else{print $1"\ty"}}' + tail -n+2 edgeR.fin.qiu.genes.count_table + awk '-F\t' 'NR==1{print "id\t"$0} NR>1{print $0}' edgeR.fin.qiu.genes.count_table + cut -f 1,6 + awk '-F\t' 'NR==1{print -1"\t"$0} NR>1{print $2"\t"$0}' + sort -k1,1g + cut -f 2- + awk '-F\t' 'FILENAME==ARGV[1]{xy[$1]=$2} FILENAME==ARGV[2]{if(FNR==1){header=$0}; res[$1]=$0} FILENAME==ARGV[3]{if(FNR==1){print header"\t"$2}else{if(xy[$1]=="x"){print res[$1]"\t"$2}}}' edgeR.fin.qiu.genes.count_table.xy input_1/fin.qiu.genes.count_table edgeR.fin.qiu.genes.count_table.p + awk '-F\t' 'FILENAME==ARGV[1]{xy[$1]=$2} FILENAME==ARGV[2]{if(FNR==1){header=$0}; res[$1]=$0} FILENAME==ARGV[3]{if(FNR==1){print header"\t"$2}else{if(xy[$1]=="y"){print res[$1]"\t"$2}}}' edgeR.fin.qiu.genes.count_table.xy input_1/fin.qiu.genes.count_table edgeR.fin.qiu.genes.count_table.p + i=result.edgeR.fin.qiu.genes.count_table.female_long.up.female_short.down.txt + sed 's/\t$//' + awk '-F\t' -v maxlen=30000 'FILENAME==ARGV[1]{for(i=1;i<=NF;i++){n=int((length($i)-1)/maxlen)+1; if(n>a[i]){a[i]=n}}} FILENAME==ARGV[2]{if(FNR==1){ORS=""; for(i=1;i<=NF;i++){if(a[i]<=1){print $i"\t"}else{for(j=1;j<=a[i];j++){print $i" (split "j")\t"}}}; print "\n"}else{for(i=1;i<=NF;i++){if(a[i]<=1){print $i"\t"}else{for(j=1;j<=a[i];j++){print substr($i,(j-1)*maxlen+1,maxlen)"\t" }}}; print "\n"}}' result.edgeR.fin.qiu.genes.count_table.female_long.up.female_short.down.txt ./result.edgeR.fin.qiu.genes.count_table.female_long.up.female_short.down.txt + i=result.edgeR.fin.qiu.genes.count_table.female_long.down.female_short.up.txt + awk '-F\t' -v maxlen=30000 'FILENAME==ARGV[1]{for(i=1;i<=NF;i++){n=int((length($i)-1)/maxlen)+1; if(n>a[i]){a[i]=n}}} FILENAME==ARGV[2]{if(FNR==1){ORS=""; for(i=1;i<=NF;i++){if(a[i]<=1){print $i"\t"}else{for(j=1;j<=a[i];j++){print $i" (split "j")\t"}}}; print "\n"}else{for(i=1;i<=NF;i++){if(a[i]<=1){print $i"\t"}else{for(j=1;j<=a[i];j++){print substr($i,(j-1)*maxlen+1,maxlen)"\t" }}}; print "\n"}}' result.edgeR.fin.qiu.genes.count_table.female_long.down.female_short.up.txt ./result.edgeR.fin.qiu.genes.count_table.female_long.down.female_short.up.txt + sed 's/\t$//' + FUNC_RUN_DOCKER c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 java -Xmx1G -jar /usr/local/bin/excel2.jar result.edgeR.fin.qiu.genes.count_table.female_long.up.female_short.down.txt.temp result.edgeR.fin.qiu.genes.count_table.female_long.up.female_short.down.txt.xlsx + PP_RUN_IMAGE=c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 + shift + PP_RUN_DOCKER_CMD=("${@}") ++ date +%Y%m%d_%H%M%S_%3N + PPDOCNAME=pp20230907_180843_389_32521 + echo pp20230907_180843_389_32521 ++ id -u ++ id -g + docker run --name pp20230907_180843_389_32521 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -u 2007:600 -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 java -Xmx1G -jar /usr/local/bin/excel2.jar result.edgeR.fin.qiu.genes.count_table.female_long.up.female_short.down.txt.temp result.edgeR.fin.qiu.genes.count_table.female_long.up.female_short.down.txt.xlsx Start converting + FUNC_RUN_DOCKER c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 java -Xmx1G -jar /usr/local/bin/excel2.jar result.edgeR.fin.qiu.genes.count_table.female_long.down.female_short.up.txt.temp result.edgeR.fin.qiu.genes.count_table.female_long.down.female_short.up.txt.xlsx + PP_RUN_IMAGE=c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 + shift + PP_RUN_DOCKER_CMD=("${@}") ++ date +%Y%m%d_%H%M%S_%3N + PPDOCNAME=pp20230907_180844_867_26212 + echo pp20230907_180844_867_26212 ++ id -u ++ id -g + docker run --name pp20230907_180844_867_26212 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR -u 2007:600 -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 java -Xmx1G -jar /usr/local/bin/excel2.jar result.edgeR.fin.qiu.genes.count_table.female_long.down.female_short.up.txt.temp result.edgeR.fin.qiu.genes.count_table.female_long.down.female_short.up.txt.xlsx Start converting + rm -f edgeR.fin.qiu.genes.count_table.id edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.x edgeR.Qiu.fin2.txt.fin.qiu.genes.count_table.edgeR.txt.fin.qiu.genes.count_table.y edgeR.fin.qiu.genes.count_table.xy edgeR.fin.qiu.genes.count_table.p result.edgeR.fin.qiu.genes.count_table.female_long.up.female_short.down.txt.temp result.edgeR.fin.qiu.genes.count_table.female_long.down.female_short.up.txt.temp + post_processing + '[' 1 = 1 ']' + rm -f /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/statistics~edgeR/pp-singularity-flag + '[' '' = y ']' + echo 0 + exit PID: 1631917