c2997108/centos6:2 centos:centos6 quay.io/biocontainers/jellyfish:2.2.10--h2d50403_0
using docker
+ cmd='jellyfish count -m 21 -o output -s 33554432 -t 8 -C'
+ for i in '$r1'
++ echo SRR1363434_1.fastq.gz
++ grep 'gz$'
++ wc -l
+ '[' 1 = 1 ']'
+ cmd='jellyfish count -m 21 -o output -s 33554432 -t 8 -C <(zcat SRR1363434_1.fastq.gz)'
+ for i in '$r1'
++ echo SRR1363434_2.fastq.gz
++ grep 'gz$'
++ wc -l
+ '[' 1 = 1 ']'
+ cmd='jellyfish count -m 21 -o output -s 33554432 -t 8 -C <(zcat SRR1363434_1.fastq.gz) <(zcat SRR1363434_2.fastq.gz)'
+ for i in '$r1'
++ echo SRR1363435_1.fastq.gz
++ grep 'gz$'
++ wc -l
+ '[' 1 = 1 ']'
+ cmd='jellyfish count -m 21 -o output -s 33554432 -t 8 -C <(zcat SRR1363434_1.fastq.gz) <(zcat SRR1363434_2.fastq.gz) <(zcat SRR1363435_1.fastq.gz)'
+ for i in '$r1'
++ echo SRR1363435_2.fastq.gz
++ grep 'gz$'
++ wc -l
+ '[' 1 = 1 ']'
+ cmd='jellyfish count -m 21 -o output -s 33554432 -t 8 -C <(zcat SRR1363434_1.fastq.gz) <(zcat SRR1363434_2.fastq.gz) <(zcat SRR1363435_1.fastq.gz) <(zcat SRR1363435_2.fastq.gz)'
+ for i in '$r1'
++ echo SRR1363436_1.fastq.gz
++ grep 'gz$'
++ wc -l
+ '[' 1 = 1 ']'
+ cmd='jellyfish count -m 21 -o output -s 33554432 -t 8 -C <(zcat SRR1363434_1.fastq.gz) <(zcat SRR1363434_2.fastq.gz) <(zcat SRR1363435_1.fastq.gz) <(zcat SRR1363435_2.fastq.gz) <(zcat SRR1363436_1.fastq.gz)'
+ for i in '$r1'
++ echo SRR1363436_2.fastq.gz
++ grep 'gz$'
++ wc -l
+ '[' 1 = 1 ']'
+ cmd='jellyfish count -m 21 -o output -s 33554432 -t 8 -C <(zcat SRR1363434_1.fastq.gz) <(zcat SRR1363434_2.fastq.gz) <(zcat SRR1363435_1.fastq.gz) <(zcat SRR1363435_2.fastq.gz) <(zcat SRR1363436_1.fastq.gz) <(zcat SRR1363436_2.fastq.gz)'
+ echo 'jellyfish count -m 21 -o output -s 33554432 -t 8 -C <(zcat SRR1363434_1.fastq.gz) <(zcat SRR1363434_2.fastq.gz) <(zcat SRR1363435_1.fastq.gz) <(zcat SRR1363435_2.fastq.gz) <(zcat SRR1363436_1.fastq.gz) <(zcat SRR1363436_2.fastq.gz)'
jellyfish count -m 21 -o output -s 33554432 -t 8 -C <(zcat SRR1363434_1.fastq.gz) <(zcat SRR1363434_2.fastq.gz) <(zcat SRR1363435_1.fastq.gz) <(zcat SRR1363435_2.fastq.gz) <(zcat SRR1363436_1.fastq.gz) <(zcat SRR1363436_2.fastq.gz)
+ eval 'DO_JELLYFISH bash -c '\''jellyfish count -m 21 -o output -s 33554432 -t 8 -C <(zcat SRR1363434_1.fastq.gz) <(zcat SRR1363434_2.fastq.gz) <(zcat SRR1363435_1.fastq.gz) <(zcat SRR1363435_2.fastq.gz) <(zcat SRR1363436_1.fastq.gz) <(zcat SRR1363436_2.fastq.gz)'\'''
++ docker run -v /data/user2/work/76/input_1:/data/user2/work/76/input_1 -w /data/user2/work/76/input_1 -u root -i --rm quay.io/biocontainers/jellyfish:2.2.10--h2d50403_0 bash -c 'jellyfish count -m 21 -o output -s 33554432 -t 8 -C <(zcat SRR1363434_1.fastq.gz) <(zcat SRR1363434_2.fastq.gz) <(zcat SRR1363435_1.fastq.gz) <(zcat SRR1363435_2.fastq.gz) <(zcat SRR1363436_1.fastq.gz) <(zcat SRR1363436_2.fastq.gz)'
+ docker run -v /data/user2/work/76/input_1:/data/user2/work/76/input_1 -w /data/user2/work/76/input_1 -u root -i --rm quay.io/biocontainers/jellyfish:2.2.10--h2d50403_0 jellyfish histo --high=33554432 output
+ rm -f output
+ echo 'library(Cairo)
a=read.table("output.txt")
CairoPNG("kmer-graph.png", width = 1000, height = 1000)
plot(a,log="xy",type="o", main="K-mer distribution", xlab="K-mer coverage", ylab="K-mer frequency", cex=0.5)
dev.off()

m=floor(log2(max(a[,1])))
c=rep(0,m+1)
for(i in 1:(dim(a)[1])){tempm=floor(log2(a[i,1])); c[tempm+1]=c[tempm+1]+a[i,1]*a[i,2]}
d=as.matrix(c)
row.names(d)=2^(0:m)
CairoPNG("kmer-base-histogram.png", width = 1000, height = 1000)
barplot(t(d),xlab = "K-mer frequency section", ylab = "K-mer frequency x coverage")
dev.off()'
+ docker run -v /data/user2/work/76/input_1:/data/user2/work/76/input_1 -w /data/user2/work/76/input_1 -u root -i --rm c2997108/centos6:2 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(Cairo)
> a=read.table("output.txt")
> CairoPNG("kmer-graph.png", width = 1000, height = 1000)
> plot(a,log="xy",type="o", main="K-mer distribution", xlab="K-mer coverage", ylab="K-mer frequency", cex=0.5)
> dev.off()
null device 
          1 
> 
> m=floor(log2(max(a[,1])))
> c=rep(0,m+1)
> for(i in 1:(dim(a)[1])){tempm=floor(log2(a[i,1])); c[tempm+1]=c[tempm+1]+a[i,1]*a[i,2]}
> d=as.matrix(c)
> row.names(d)=2^(0:m)
> CairoPNG("kmer-base-histogram.png", width = 1000, height = 1000)
> barplot(t(d),xlab = "K-mer frequency section", ylab = "K-mer frequency x coverage")
> dev.off()
null device 
          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/76/input_1:/data/user2/work/76/input_1 -w /data/user2/work/76/input_1 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit