edgeR analysis
gene_id 0010_1.fastq 0012_1.fastq 0014_1.fastq 0015_1.fastq 0016_1.fastq 0017_1.fastq 0021_1.fastq 0024_1.fastq 0025_1.fastq 0026_1.fastq 0032_1.fastq 0035_1.fastq 0041_1.fastq 0042_1.fastq 0046_1.fastq 0050_1.fastq 0063_1.fastq 0066_1.fastq 0067_1.fastq 0069_1.fastq 0073_1.fastq 0074_1.fastq 0080_1.fastq 0081_1.fastq 0083_1.fastq 0085_1.fastq 0086_1.fastq 0087_1.fastq 0088_1.fastq 0089_1.fastq 0094_1.fastq 0095_1.fastq 0096_1.fastq 0097_1.fastq 0098_1.fastq 0102_1.fastq 0103_1.fastq 0104_1.fastq 9250_1.fastq 9303_1.fastq fin8220_1.fastq fin8241_1.fastq
MSTRG.34956 0 0 1.67825 0.841872 0.51571 0 0 0 0 0 1.19179 0 0 0 0 0 2.22818 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.58743 0 0 0 0 2.16523 0 0 0 0 0
MSTRG.33635 0.8125 0 0 0 0.952206 0 1.02941 0.084559 0 0.555147 1.14016 0.371324 0 1.03676 2.20588 0.503676 0 0.055147 1.52941 0 0 0 0 5.45221 0 0.191176 0 0 0.088235 0 0 0.058824 0 0.966912 0 0.669118 1.57721 2.61029 0 0 0 0
MSTRG.34957 0 0.349481 0 0 0 0 0 0 0 0 0 0 0 0 0 0.279123 0.920415 0 0 0 0 0 0 0.179931 0 0 0 0 0 0 0 0 0 0.219723 3.35294 0 0 0 0 0 0 0
MSTRG.33636 0.517241 0 0 0 0 0.52069 0 0.517241 0 0 1.47759 0.517241 0 0.510345 0.455172 0.496552 0 0 1.53965 0 0.255172 0 0 0 0 0 0.512069 0 0 0 0 0 0.194828 0.437931 0.025862 0.517241 1.23104 1.06724 0.225862 0 1.13597 0.218966
MSTRG.34958 0.476948 0 0 0 0 0.91256 0.329094 0 0 0 0 0.45151 0.45787 0 0 0.952305 0.839428 0.403816 1.8601 0 0.235294 0.475358 0 0.470588 0 0.146264 0.440382 0 0.699523 2.12719 0.236884 0.267091 0.620032 0.915739 0 0.406995 0.91097 0.244833 1.37997 0 0.922099 0
MSTRG.33637 8.76232 14.7562 7.40916 15.2814 11.9498 7.58117 5.27547 19.5882 8.16143 4.63251 9.4 6.13842 7.48348 11.8151 6.73134 13.8355 13.1805 7.16488 12.4116 4.40255 4.95846 11.1834 7.56257 11.8422 7.06995 10.0331 9.8606 9.28109 8.04729 13.3893 7.5768 4.89631 6.78818 10.9112 8.54253 11.2956 9.72315 8.13215 12.1456 5.36823 10.9889 10.7606
MSTRG.34959 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MSTRG.33638 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.37895 0 0 1.42749 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MSTRG.32000 48.3219 56.5226 38.3145 67.8422 73.1224 32.1719 49.1824 88.3027 37.3264 36.0939 50.4939 52.2885 52.2132 52.5532 36.7729 85.1511 37.2282 54.4083 56.4022 23.0667 18.1345 59.9655 50.6956 72.1771 40.3438 38.1944 59.5931 33.2765 42.9829 91.9969 61.339 40.5121 51.9577 67.4603 50.278 67.3721 50.8645 36.9446 62.7158 34.0289 49.6916 33.7935
id condition
0010_1.fastq male_short
0016_1.fastq female_short
0021_1.fastq female_long
0024_1.fastq male_long
0032_1.fastq male_long
0035_1.fastq female_short
0050_1.fastq female_short
0063_1.fastq female_short
0069_1.fastq male_long
id condition
0010_1.fastq.gz male_short
0016_1.fastq.gz female_short
0021_1.fastq.gz female_long
0024_1.fastq.gz male_long
0032_1.fastq.gz male_long
0035_1.fastq.gz female_short
0050_1.fastq.gz female_short
0063_1.fastq.gz female_short
0069_1.fastq.gz male_long
statistics~edgeR -c 8 -m 32 input_1/fin.qiu.genes.count_table input_2/Qiu.fin2.txt
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