script: /data/user2/work/80/statistics~edgeR "$scriptdir"/statistics~scatter_with_variance
c2997108/centos6:3 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 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.1week_A1_1.fq.gz.1week_A2_1.fq.gz.go.R
+ inputsamplematrix=sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ inputmatrix=kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ g1=1week_A1_1.fq.gz
+ g2=1week_A2_1.fq.gz
+ '[' 1week_A1_1.fq.gz = '' ']'
+ '[' 1week_A2_1.fq.gz = '' ']'
+ p=0.05
++ basename kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ outputfile=edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
++ basename sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
++ basename kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ samplex=edgeR.sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.x
++ basename sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
++ basename kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ sampley=edgeR.sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.y
++ basename kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ outputfilexup=result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.up.1week_A2_1.fq.gz.down.txt
++ basename kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ outputfileyup=result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.down.1week_A2_1.fq.gz.up.txt
+ '[' Trinotate.xls3.go.cnt = '' ']'
+ annotationfile=Trinotate.xls3.go.cnt
++ awk '-F\t' -v g1=1week_A1_1.fq.gz -v g2=1week_A2_1.fq.gz '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[$i]==g2){print "2,"}else{print "3,"}}}' sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
++ sed 's/,$//'
+ gp=1,2
+ cat
+ docker run -v /data/user2/work/80:/data/user2/work/80 -w /data/user2/work/80 -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 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("kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt",sep="\t",header=T,row.names=1))
> group <- factor(c(1,2))
> y <- DGEList(counts=x,group=group)
> y <- calcNormFactors(y)
> design <- model.matrix(~group)
> y <- estimateDisp(y,design)
Warning message:
In estimateDisp.default(y = y$counts, design = design, group = group,  :
  No residual df: setting dispersion to NA
> fit <- glmQLFit(y,design)
Error in glmFit.default(y, design = design, dispersion = dispersion, offset = offset,  : 
  dispersion must be numeric
Calls: glmQLFit ... glmQLFit -> glmQLFit.default -> glmFit -> glmFit.default
Execution halted
+ true
+ '[' '!' -e edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt ']'
+ touch edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ awk '-F\t' 'NR>1{print $1}' edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ awk '-F\t' -v g1=1week_A1_1.fq.gz '$2==g1{print $1}' sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ awk '-F\t' -v g2=1week_A2_1.fq.gz '$2==g2{print $1}' sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ bash /data/user2/work/80/statistics~scatter_with_variance -x 1week_A1_1.fq.gz -y 1week_A2_1.fq.gz kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id edgeR.sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.x edgeR.sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.y
c2997108/centos6:3 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 centos:centos6
using docker
+ set -o pipefail
+ countmat=kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ sigmat=edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id
+ listx=edgeR.sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.x
+ listy=edgeR.sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.y
+ label_x=1week_A1_1.fq.gz
+ label_y=1week_A2_1.fq.gz
+ p=0.05
++ basename kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
++ basename edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id
+ output=kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id
+ cat kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ awk '-F\t' 'FILENAME==ARGV[1]{if(FNR>1){for(i=2;i<=NF;i++){a[i]+=$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 kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ cat edgeR.sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.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 kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm
+ cat edgeR.sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.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 kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm
+ cat edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id
+ awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=1} FILENAME==ARGV[2] && (FNR==1 || a[$1]==1){print $0}' /dev/stdin kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm_x
+ cat edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id
+ awk '-F\t' 'FILENAME==ARGV[1]{a[$1]=1} FILENAME==ARGV[2] && (FNR==1 || a[$1]==1){print $0}' /dev/stdin kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm_y
+ cat
+ docker run -v /data/user2/work/80:/data/user2/work/80 -w /data/user2/work/80 -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 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="1week_A1_1.fq.gz"
> label_y="1week_A2_1.fq.gz"
> file_data_x="kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm_x"
> file_data_y="kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm_y"
> file_sig_data_x="kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm_x_sig"
> file_sig_data_y="kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.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("kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.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+(end_class-start_class)/(num_class-2))
+   xt=plot_mean_data_x[n]
+   yt=plot_mean_data_y[n]
+   par(new=T)
+   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),axes=F,xlab="",ylab="")
+  }
+  k=num_class-1
+  i=min(total_var_data)
+  n=(total_var_data>=i & total_var_data<start_class)
+  xt=plot_mean_data_x[n]
+  yt=plot_mean_data_y[n]
+  par(new=T)
+  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),axes=F,xlab="",ylab="")
+ 
+  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="")
+ 
+  plot(c(0,0),c(-1,num_class),xlim=c(0,0),ylim=c(-1,num_class),cex=0,bty="n",axes=F,xlab="",ylab="")
+  for(k in 0:(num_class-2)){
+   i=end_class+(start_class-end_class)*k/(num_class-2)
+   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)
+  }
+  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("kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.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 kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm_x kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm_y kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm_x_sig kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id.cpm_y_sig
+ post_processing
+ '[' 3 = 1 ']'
+ exit
+ tail -n+2 edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ awk '{if($2<=0){print $1"\tx"}else{print $1"\ty"}}'
+ awk '-F\t' 'NR==1{print "id\t"$0} NR>1{print $0}' edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt
+ 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.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.xy Trinotate.xls3.go.cnt edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.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"$2}}}' edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.xy Trinotate.xls3.go.cnt edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.p
+ i=result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.up.1week_A2_1.fq.gz.down.txt
+ sed 's/\t$//'
+ 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.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.up.1week_A2_1.fq.gz.down.txt ./result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.up.1week_A2_1.fq.gz.down.txt
+ i=result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.down.1week_A2_1.fq.gz.up.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.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.down.1week_A2_1.fq.gz.up.txt ./result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.down.1week_A2_1.fq.gz.up.txt
+ docker run -v /data/user2/work/80:/data/user2/work/80 -w /data/user2/work/80 -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 java -Xmx1G -jar /usr/local/bin/excel2.jar result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.up.1week_A2_1.fq.gz.down.txt.temp result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.up.1week_A2_1.fq.gz.down.txt.xlsx
Start converting
+ docker run -v /data/user2/work/80:/data/user2/work/80 -w /data/user2/work/80 -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 java -Xmx1G -jar /usr/local/bin/excel2.jar result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.down.1week_A2_1.fq.gz.up.txt.temp result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.down.1week_A2_1.fq.gz.up.txt.xlsx
Start converting
+ rm -f edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.id edgeR.sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.x edgeR.sample.input.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.y edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.xy edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.p result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.up.1week_A2_1.fq.gz.down.txt.temp result.edgeR.kallisto.go.counts.matrix.1week_A1_1.fq.gz.1week_A2_1.fq.gz.txt.1week_A1_1.fq.gz.down.1week_A2_1.fq.gz.up.txt.temp
+ post_processing
+ '[' 2 = 1 ']'
+ exit