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 singularity
+ set -o pipefail
++ echo input_1/output.vcf
++ wc -l
++ grep '[.]gz$'
++ true
+ '[' 0 = 1 ']'
+ vcf=input_1/output.vcf
++ basename input_1/output.vcf
+ out='output.vcf .vcf'
+ cat input_1/output.vcf
+ grep -v '^##'
+ sed 's/\t$//'
+ awk -v gq=10 '-F\t' '
 {ORS="\t"; print $1"\t"$2"\t"$4"\t"$5"\t"$6"\t"$8;
  for(i=10;i<=NF;i++){split($i,arr,":"); if(NR==1){print $i}else{if(arr[4]>=gq){print arr[1]}else{print "./."}}}; ORS="\n"; print ""
 }'
+ awk '-F\t' '{n=0;for(i=7;i<=NF;i++){if($i=="./."){n++}}; if(n<NF-6){print $0}}'
++ cat output.tsv
++ wc -l
+ '[' 32146 -lt 1000000 ']'
+ singularity exec -B /suikou/files/m64g/user2/work/yoshitake/112:/mnt --pwd /mnt /home/user2/img/c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_4-kegg_4 java -jar /usr/local/bin/excel2.jar output.tsv output.xlsx
Start converting
+ grep -v '[.]/[.]' output.tsv
+ sed 's/\t$//'
+ awk '-F\t' '
 NR==1{ORS="\t"; print $1":"$2":"$3":"$4; for(i=7;i<=NF;i++){print $i}; ORS="\n"; print ""}
 NR>1{ORS="\t"; print $1":"$2":"$3":"$4; for(i=7;i<=NF;i++){split($i,arr2,"/"); if(arr2[1]>1){arr2[1]=1}; if(arr2[2]>1){arr2[2]=1}; print arr2[1]+arr2[2]}; ORS="\n"; print ""}
'
+ cut -f 2- output.nonNA.txt
++ head -n 1 output.tsv
++ awk '-F\t' '{if((NF-6)/10<8){print 8}else{print (NF-6)/10}}'
+ w=8
++ head -n 1 output.tsv
++ awk '-F\t' '{if((NF-6)/10<8){print 4}else{print (NF-6)/20}}'
+ h=4
+ echo 'a=read.table('\''output.nonNA.tsv'\'',sep='\''\t'\'',header=T)
c=cor(a); for(i in 1:ncol(c)){c[is.na(c[,i]),i]=0}; result=hclust(as.dist(1-c),'\''ave'\'')
pdf('\''sample-relation.pdf'\'',width=8, height=4, pointsize=2)
plot(result)
dev.off()'
+ singularity exec -B /suikou/files/m64g/user2/work/yoshitake/112:/mnt --pwd /mnt /home/user2/img/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)

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You are welcome to redistribute it under certain conditions.
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  Natural language support but running in an English locale

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> a=read.table('output.nonNA.tsv',sep='\t',header=T)
> c=cor(a); for(i in 1:ncol(c)){c[is.na(c[,i]),i]=0}; result=hclust(as.dist(1-c),'ave')
> pdf('sample-relation.pdf',width=8, height=4, pointsize=2)
> plot(result)
> dev.off()
null device 
          1 
> 
+ post_processing
+ '[' 1 = 1 ']'
+ '[' 'singularity exec -B /suikou/files/m64g/user2/work/yoshitake/112:/mnt --pwd /mnt /home/user2/img/' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']'
+ echo 0
+ exit