Create a graph of coverage and contig length to check the contamination of the assembled contig with minimap2 for long reads.
>NODE_1_length_136573_cov_91.117457
AACACACTGTCACTTGACGCAGGGCTGAAAGTTCTACAGCAACGGTATACCAATATGATA
ATGGTTTACTAAATTTTCTGGGGATCCCTCAGCAGTAATCCCCCCTCTTCAACCTGAACT
TCATGCGACGGTGCATATTGCTGTTCCACCGGCAGTTCGGGATCTTCCCGATGTTCCAGC
AATTCAGGCTGTTCGCACAGCTTGCGATGCAACGAACCACCGGTTGCCACCACCAGTTCC
TGTAAACCCCGGCAGATGGCGAAAATGGGGATGCGCCTTTCGAGTGCGGCATTAATTAAC
GCCATGCTCAGAAGATCACGCCCGGGATCGGCGTCAGGCTCATCGCCGTTTTCACCATAT
AGGTGCGGCTGCACATTGCTGGGACTACCAGGAAGATAAATGCCATCGAGTTTCGGCAAA
AGTTGTTCAAGTAAGGACGGTTCCGCCAGCGCATGTGGCAGCGCAATTGGCAAACCGCCT
GCGTGGATGATGGCATTCAGGTACTTTTCTTGCAGAGTCTGGGTCGCATGACCCTTAAGC
@DRR015801.1 HWI-ST895:156:C1HNFACXX:1:1101:2347:1967/1
NACATCATCACATCGCTGGGCTGTCTGGAAGGTGGTGACCTGGATATCGCTTATCTTTCTGAAATTGACCCCACCTGGACGGACAGCAGCCTGACCACCA
+
#1:DDDFFHGHHHJJIJJBHIJJIHIJJJIJJ?DGDHIJJJIJIJJJJJJJJJJJJJJJIJIIJHHHHHHFFFDDCEDDDDDDDDDDDDDDDDDDDDDDD
@DRR015801.2 HWI-ST895:156:C1HNFACXX:1:1101:2281:1982/1
NTATCTTGCTATCCCCAAAAAATTCAGAGATGAGTCGAAAGTCATATCTTTCATGTATGATAAGAATAAAACGTATATTTTGCTATTTTTGATTGCTTTT
+
#1=DDFFFHHHHHJJJJJJJJJJJJJJJIIJJIIHIIJIJJEHIJJJIJJJIJJJGIJJJJJIJIJJJJJHHHHFBFFFFEEEEEEEEDD@DDDDDDDDC
@DRR015801.3 HWI-ST895:156:C1HNFACXX:1:1101:2751:1963/1
NAGAAACCTCCTGAGATCACCCTGAAAAGAATAGGAGAGGAGGCGGGTAAAATCTATATGATACAGAGACAACGATGTTCCCGCTGTGGGACACAGCGGG
@DRR015801.1 HWI-ST895:156:C1HNFACXX:1:1101:2347:1967/2
GCATATTAAAGGCGCTGGCAATGGCATCTGCTGCACAGGCCCCCTGTGCTATCGGATTGGCAAAGATGACAGCTTCCGGATTGAGAATGGTGGTCAGGCT
+
CCCFFFFFHHHGGJIJIJJJJIJJJJIJJIICGGJJIGIJJJIJHIHIIGFGGIJGHHCDEFFECCCECEDCACDDDDDBBB<ACBDDCC4@B5CCDDD@
@DRR015801.2 HWI-ST895:156:C1HNFACXX:1:1101:2281:1982/2
GTGTATGGGCAAATGAAACCATTGAAAAAGCAATCAAAAATAGCAAAATATACGTTTTATTCTTATCATACATGAAAGATATGACTTTCGACTCATCTCT
+
@BCDFFFFHHHHHJJJJJJJJJJIJGJIHGHIJJJJJJJJIJIJJJJIJJHIIIGIJJIJJIJJIIJJJIJJJIHHHHHFFFFFFFFEEDDDDDDDDDDE
@DRR015801.3 HWI-ST895:156:C1HNFACXX:1:1101:2751:1963/2
CAGTCGATCAATAATATTCCACTGGATGCGCGTAATCACGGCTATACGGTGCTGGATATTCAGCAAGACGGGCCGACCATTCGTTATTTAATTCAGAAAT
post-assemble~coverage-length-graph_by-minimap2 -c 16 -m 32 -x true input_1/scaffolds.fasta input_2
pp post-assemble~coverage-length-graph_by-minimap2 -c 16 -m 32 -x true input_1/scaffolds.fasta input_2
PID: 2037361
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'post-assemble~coverage-length-graph_by-minimap2' -c 16 -m 32 -x true input_1/scaffolds.fasta input_2
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/post-assemble~coverage-length-graph_by-minimap2
Containers: c2997108/centos6:2-bwa-0.7.17-r1198-dirty c2997108/ubuntu20:R-2_gplots centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/samtools:1.19--h50ea8bc_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ ref=input_1/scaffolds.fasta
+ '[' '!' -e input_1/scaffolds.fasta.fai ']'
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ find input_2/ -maxdepth 1
++ egrep '[.]f(ast|)q(|[.]gz)$'
+ for i in `find $input_2/ -maxdepth 1 |egrep '[.]f(ast|)q(|[.]gz)$' || true`
++ basename input_2/test_1.fq
+ i2=test_1.fq
++ basename input_2/test_1.fq
++ sed 's/[.]f\(ast\|\)q.*//'
+ samplename=test_1
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -t 16 -ax map-ont '\''input_1/scaffolds.fasta'\'' '\''input_2/test_1.fq'\'' | ( PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -h -F 0x800 ) > '\''test_1.fq.sam'\'''
+ for i in `find $input_2/ -maxdepth 1 |egrep '[.]f(ast|)q(|[.]gz)$' || true`
++ basename input_2/test_2.fq
+ i2=test_2.fq
++ basename input_2/test_2.fq
++ sed 's/[.]f\(ast\|\)q.*//'
+ samplename=test_2
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -t 16 -ax map-ont '\''input_1/scaffolds.fasta'\'' '\''input_2/test_2.fq'\'' | ( PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -h -F 0x800 ) > '\''test_2.fq.sam'\'''
[M::mm_idx_gen::0.240*1.22] collected minimizers
[M::mm_idx_gen::0.292*2.29] sorted minimizers
[M::main::0.293*2.29] loaded/built the index for 2111 target sequence(s)
[M::mm_mapopt_update::0.323*2.16] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2111
[M::mm_idx_stat::0.339*2.10] distinct minimizers: 955730 (97.96% are singletons); average occurrences: 1.039; average spacing: 5.390; total length: 5354294
[M::worker_pipeline::0.470*3.29] mapped 10000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -t 16 -ax map-ont input_1/scaffolds.fasta input_2/test_1.fq
[M::main] Real time: 0.491 sec; CPU: 1.567 sec; Peak RSS: 0.070 GB
[M::mm_idx_gen::0.209*1.25] collected minimizers
[M::mm_idx_gen::0.294*1.60] sorted minimizers
[M::main::0.295*1.60] loaded/built the index for 2111 target sequence(s)
[M::mm_mapopt_update::0.322*1.55] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2111
[M::mm_idx_stat::0.349*1.51] distinct minimizers: 955730 (97.96% are singletons); average occurrences: 1.039; average spacing: 5.390; total length: 5354294
[M::worker_pipeline::0.465*2.78] mapped 10000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -t 16 -ax map-ont input_1/scaffolds.fasta input_2/test_2.fq
[M::main] Real time: 0.486 sec; CPU: 1.314 sec; Peak RSS: 0.079 GB
+ cat
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots bash run-cleanup.sh "test_1.fq.sam" "0.3" "0" "input_1/scaffolds.fasta"'
+ xargs '-d\n' -I '{}' -P 16 bash -c '{}'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots bash run-cleanup.sh "test_2.fq.sam" "0.3" "0" "input_1/scaffolds.fasta"'
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("test_1.fq.sam2.cov",sep="\t",row.names=1);
> CairoPNG(file="test_1.fq.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
Error in rep.int(i.multi, number[number > 1]) : invalid 'times' value
Calls: sunflowerplot -> sunflowerplot.default
Execution halted
> library(Cairo); a=read.table("test_2.fq.sam2.cov",sep="\t",row.names=1);
> CairoPNG(file="test_2.fq.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
Error in rep.int(i.multi, number[number > 1]) : invalid 'times' value
Calls: sunflowerplot -> sunflowerplot.default
Execution halted
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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); data=read.table("test_1.fq.sam2.cov.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="test_1.fq.sam2.cov.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
> library(Cairo); data=read.table("test_2.fq.sam2.cov.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="test_2.fq.sam2.cov.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
null device
1
>
null device
1
>
++ basename input_1/scaffolds.fasta
+ outname=scaffolds.fasta
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME!=ARGV[1]{bases[$1]+=$3} END{print "id\tcoverage\tmapped bases\tlength"; for(i in len){if(bases[i]>0){print i"\t"bases[i]/len[i]"\t"bases[i]+0"\t"len[i]}}}' input_1/scaffolds.fasta.fai test_1.fq.sam2.cov test_2.fq.sam2.cov
+ echo 'library(Cairo); a=read.table("scaffolds.fasta.output.txt",header = TRUE,sep="\t",row.names=1); CairoPNG(file="scaffolds.fasta.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()'
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots R --vanilla
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_132919_757_24775
+ echo pp20250302_132919_757_24775
++ id -u
++ id -g
+ docker run --name pp20250302_132919_757_24775 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots R --vanilla
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("scaffolds.fasta.output.txt",header = TRUE,sep="\t",row.names=1); CairoPNG(file="scaffolds.fasta.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
null device
1
>
+ tail -n+2 scaffolds.fasta.output.txt
+ awk '-F\t' -v l=0.99 '{cnt[int($2)]+=$4; total+=$4; if(int($2)>max){max=int($2)}} END{for(i=1;i<=max;i++){print i"\t"cnt[i]+0; s+=cnt[i]; if(s>=total*l){print "over_"i"\t"total-s; break}}}'
+ echo 'library(Cairo); data=read.table("scaffolds.fasta.output.txt.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="scaffolds.fasta.output.txt.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()'
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots R --vanilla
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_132920_664_31325
+ echo pp20250302_132920_664_31325
++ id -u
++ id -g
+ docker run --name pp20250302_132920_664_31325 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots R --vanilla
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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); data=read.table("scaffolds.fasta.output.txt.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="scaffolds.fasta.output.txt.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
null device
1
>
+ '[' true = true ']'
+ cat
+ for i in *.sam
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 bash run-makebam.sh "test_1.fq.sam" "16"'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 bash run-makebam.sh "test_2.fq.sam" "16"'
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
+ '[' true = true ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.19--h50ea8bc_0 merge scaffolds.fasta.bam test_1.fq.sam.clean.bam test_2.fq.sam.clean.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.19--h50ea8bc_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_132925_190_9609
+ echo pp20250302_132925_190_9609
++ id -u
++ id -g
+ docker run --name pp20250302_132925_190_9609 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 merge scaffolds.fasta.bam test_1.fq.sam.clean.bam test_2.fq.sam.clean.bam
/usr/local/env-execute: line 3: exec: merge: not found
PID: 2039963
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'post-assemble~coverage-length-graph_by-minimap2' -c 16 -m 32 -x true input_1/scaffolds.fasta input_2
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/post-assemble~coverage-length-graph_by-minimap2
Containers: c2997108/centos6:2-bwa-0.7.17-r1198-dirty c2997108/ubuntu20:R-2_gplots centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/samtools:1.19--h50ea8bc_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ ref=input_1/scaffolds.fasta
+ '[' '!' -e input_1/scaffolds.fasta.fai ']'
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ find input_2/ -maxdepth 1
++ egrep '[.]f(ast|)q(|[.]gz)$'
+ for i in `find $input_2/ -maxdepth 1 |egrep '[.]f(ast|)q(|[.]gz)$' || true`
++ basename input_2/test_1.fq
+ i2=test_1.fq
++ basename input_2/test_1.fq
++ sed 's/[.]f\(ast\|\)q.*//'
+ samplename=test_1
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -t 16 -ax map-ont '\''input_1/scaffolds.fasta'\'' '\''input_2/test_1.fq'\'' | ( PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -h -F 0x800 ) > '\''test_1.fq.sam'\'''
+ for i in `find $input_2/ -maxdepth 1 |egrep '[.]f(ast|)q(|[.]gz)$' || true`
++ basename input_2/test_2.fq
+ i2=test_2.fq
++ basename input_2/test_2.fq
++ sed 's/[.]f\(ast\|\)q.*//'
+ samplename=test_2
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -t 16 -ax map-ont '\''input_1/scaffolds.fasta'\'' '\''input_2/test_2.fq'\'' | ( PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -h -F 0x800 ) > '\''test_2.fq.sam'\'''
[M::mm_idx_gen::0.205*1.19] collected minimizers
[M::mm_idx_gen::0.257*2.36] sorted minimizers
[M::main::0.258*2.35] loaded/built the index for 2111 target sequence(s)
[M::mm_mapopt_update::0.286*2.22] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2111
[M::mm_idx_stat::0.302*2.16] distinct minimizers: 955730 (97.96% are singletons); average occurrences: 1.039; average spacing: 5.390; total length: 5354294
[M::worker_pipeline::0.477*2.74] mapped 10000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -t 16 -ax map-ont input_1/scaffolds.fasta input_2/test_1.fq
[M::main] Real time: 0.497 sec; CPU: 1.328 sec; Peak RSS: 0.067 GB
[M::mm_idx_gen::0.217*1.26] collected minimizers
[M::mm_idx_gen::0.270*2.28] sorted minimizers
[M::main::0.270*2.28] loaded/built the index for 2111 target sequence(s)
[M::mm_mapopt_update::0.297*2.16] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2111
[M::mm_idx_stat::0.314*2.10] distinct minimizers: 955730 (97.96% are singletons); average occurrences: 1.039; average spacing: 5.390; total length: 5354294
[M::worker_pipeline::0.432*3.26] mapped 10000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -t 16 -ax map-ont input_1/scaffolds.fasta input_2/test_2.fq
[M::main] Real time: 0.446 sec; CPU: 1.421 sec; Peak RSS: 0.071 GB
+ cat
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots bash run-cleanup.sh "test_1.fq.sam" "0.3" "0" "input_1/scaffolds.fasta"'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots bash run-cleanup.sh "test_2.fq.sam" "0.3" "0" "input_1/scaffolds.fasta"'
+ xargs '-d\n' -I '{}' -P 16 bash -c '{}'
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("test_2.fq.sam2.cov",sep="\t",row.names=1);
> library(Cairo); a=read.table("test_1.fq.sam2.cov",sep="\t",row.names=1);
> CairoPNG(file="test_2.fq.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
> CairoPNG(file="test_1.fq.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
Error in rep.int(i.multi, number[number > 1]) : invalid 'times' value
Calls: sunflowerplot -> sunflowerplot.default
Execution halted
Error in rep.int(i.multi, number[number > 1]) : invalid 'times' value
Calls: sunflowerplot -> sunflowerplot.default
Execution halted
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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); data=read.table("test_2.fq.sam2.cov.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="test_2.fq.sam2.cov.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
> library(Cairo); data=read.table("test_1.fq.sam2.cov.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="test_1.fq.sam2.cov.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
null device
1
>
null device
1
>
++ basename input_1/scaffolds.fasta
+ outname=scaffolds.fasta
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME!=ARGV[1]{bases[$1]+=$3} END{print "id\tcoverage\tmapped bases\tlength"; for(i in len){if(bases[i]>0){print i"\t"bases[i]/len[i]"\t"bases[i]+0"\t"len[i]}}}' input_1/scaffolds.fasta.fai test_1.fq.sam2.cov test_2.fq.sam2.cov
+ echo 'library(Cairo); a=read.table("scaffolds.fasta.output.txt",header = TRUE,sep="\t",row.names=1); CairoPNG(file="scaffolds.fasta.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()'
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots R --vanilla
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133000_952_11087
+ echo pp20250302_133000_952_11087
++ id -u
++ id -g
+ docker run --name pp20250302_133000_952_11087 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots R --vanilla
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("scaffolds.fasta.output.txt",header = TRUE,sep="\t",row.names=1); CairoPNG(file="scaffolds.fasta.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
null device
1
>
+ awk '-F\t' -v l=0.99 '{cnt[int($2)]+=$4; total+=$4; if(int($2)>max){max=int($2)}} END{for(i=1;i<=max;i++){print i"\t"cnt[i]+0; s+=cnt[i]; if(s>=total*l){print "over_"i"\t"total-s; break}}}'
+ tail -n+2 scaffolds.fasta.output.txt
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots R --vanilla
+ echo 'library(Cairo); data=read.table("scaffolds.fasta.output.txt.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="scaffolds.fasta.output.txt.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()'
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133002_113_32098
+ echo pp20250302_133002_113_32098
++ id -u
++ id -g
+ docker run --name pp20250302_133002_113_32098 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots R --vanilla
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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); data=read.table("scaffolds.fasta.output.txt.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="scaffolds.fasta.output.txt.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
null device
1
>
+ '[' true = true ']'
+ cat
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 bash run-makebam.sh "test_1.fq.sam" "16"'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 bash run-makebam.sh "test_2.fq.sam" "16"'
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
+ '[' true = true ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools merge scaffolds.fasta.bam test_1.fq.sam.clean.bam test_2.fq.sam.clean.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.19--h50ea8bc_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133006_234_14464
+ echo pp20250302_133006_234_14464
++ id -u
++ id -g
+ docker run --name pp20250302_133006_234_14464 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools merge scaffolds.fasta.bam test_1.fq.sam.clean.bam test_2.fq.sam.clean.bam
+ tail -n+2
+ sed s/,//g
+ awk '{a+=$5} END{print a}'
++ find input_2 -maxdepth 1
++ egrep '[.]f(ast|)q(|[.]gz)$'
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:0.12.1--0 seqkit stats input_2/test_1.fq input_2/test_2.fq
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:0.12.1--0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133007_379_8462
+ echo pp20250302_133007_379_8462
++ id -u
++ id -g
+ docker run --name pp20250302_133007_379_8462 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit stats input_2/test_1.fq input_2/test_2.fq
+ tail -n+2 scaffolds.fasta.output.txt
+ sort -k4,4nr -t ' '
+ awk -v n=20 'NR<=n{a+=$2} END{print a/n}'
++ cat temp.txt
++ cat temp2.txt
+ awk -v total=2000000 -v depth=0.231009 -v n=20 'BEGIN{print "Total bases of input reads: "total" bp"; print "Average depth of the longest "n" contigs: "depth" x"; print "Estimated genome size: "total / depth" bp"}'
+ rm -f temp.txt temp2.txt
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 2042773
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'post-assemble~coverage-length-graph_by-minimap2' -c 16 -m 32 -x true input_1/scaffolds.fasta input_2
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/post-assemble~coverage-length-graph_by-minimap2
Containers: c2997108/centos6:2-bwa-0.7.17-r1198-dirty c2997108/ubuntu20:R-2_gplots centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/samtools:1.19--h50ea8bc_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ ref=input_1/scaffolds.fasta
+ '[' '!' -e input_1/scaffolds.fasta.fai ']'
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ find input_2/ -maxdepth 1
++ egrep '[.]f(ast|)q(|[.]gz)$'
+ for i in `find $input_2/ -maxdepth 1 |egrep '[.]f(ast|)q(|[.]gz)$' || true`
++ basename input_2/test_1.fq
+ i2=test_1.fq
++ basename input_2/test_1.fq
++ sed 's/[.]f\(ast\|\)q.*//'
+ samplename=test_1
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -t 16 -ax map-ont '\''input_1/scaffolds.fasta'\'' '\''input_2/test_1.fq'\'' | ( PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -h -F 0x800 ) > '\''test_1.fq.sam'\'''
+ for i in `find $input_2/ -maxdepth 1 |egrep '[.]f(ast|)q(|[.]gz)$' || true`
++ basename input_2/test_2.fq
+ i2=test_2.fq
++ basename input_2/test_2.fq
++ sed 's/[.]f\(ast\|\)q.*//'
+ samplename=test_2
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -t 16 -ax map-ont '\''input_1/scaffolds.fasta'\'' '\''input_2/test_2.fq'\'' | ( PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -h -F 0x800 ) > '\''test_2.fq.sam'\'''
[M::mm_idx_gen::0.188*1.28] collected minimizers
[M::mm_idx_gen::0.245*2.55] sorted minimizers
[M::main::0.246*2.55] loaded/built the index for 2111 target sequence(s)
[M::mm_mapopt_update::0.273*2.39] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2111
[M::mm_idx_stat::0.296*2.29] distinct minimizers: 955730 (97.96% are singletons); average occurrences: 1.039; average spacing: 5.390; total length: 5354294
[M::worker_pipeline::0.443*2.99] mapped 10000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -t 16 -ax map-ont input_1/scaffolds.fasta input_2/test_1.fq
[M::main] Real time: 0.461 sec; CPU: 1.342 sec; Peak RSS: 0.069 GB
[M::mm_idx_gen::0.204*1.19] collected minimizers
[M::mm_idx_gen::0.256*2.36] sorted minimizers
[M::main::0.256*2.36] loaded/built the index for 2111 target sequence(s)
[M::mm_mapopt_update::0.280*2.24] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2111
[M::mm_idx_stat::0.299*2.16] distinct minimizers: 955730 (97.96% are singletons); average occurrences: 1.039; average spacing: 5.390; total length: 5354294
[M::worker_pipeline::0.411*3.46] mapped 10000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -t 16 -ax map-ont input_1/scaffolds.fasta input_2/test_2.fq
[M::main] Real time: 0.427 sec; CPU: 1.438 sec; Peak RSS: 0.070 GB
+ cat
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots bash run-cleanup.sh "test_1.fq.sam" "0.3" "0" "input_1/scaffolds.fasta"'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots bash run-cleanup.sh "test_2.fq.sam" "0.3" "0" "input_1/scaffolds.fasta"'
+ xargs '-d\n' -I '{}' -P 16 bash -c '{}'
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("test_1.fq.sam2.cov",sep="\t",row.names=1);
> CairoPNG(file="test_1.fq.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
> library(Cairo); a=read.table("test_2.fq.sam2.cov",sep="\t",row.names=1);
> CairoPNG(file="test_2.fq.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
Error in rep.int(i.multi, number[number > 1]) : invalid 'times' value
Calls: sunflowerplot -> sunflowerplot.default
Execution halted
Error in rep.int(i.multi, number[number > 1]) : invalid 'times' value
Calls: sunflowerplot -> sunflowerplot.default
Execution halted
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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); data=read.table("test_1.fq.sam2.cov.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="test_1.fq.sam2.cov.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
> library(Cairo); data=read.table("test_2.fq.sam2.cov.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="test_2.fq.sam2.cov.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
null device
1
>
null device
1
>
++ basename input_1/scaffolds.fasta
+ outname=scaffolds.fasta
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME!=ARGV[1]{bases[$1]+=$3} END{print "id\tcoverage\tmapped bases\tlength"; for(i in len){if(bases[i]>0){print i"\t"bases[i]/len[i]"\t"bases[i]+0"\t"len[i]}}}' input_1/scaffolds.fasta.fai test_1.fq.sam2.cov test_2.fq.sam2.cov
+ echo 'library(Cairo); a=read.table("scaffolds.fasta.output.txt",header = TRUE,sep="\t",row.names=1); CairoPNG(file="scaffolds.fasta.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()'
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots R --vanilla
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133047_586_25684
+ echo pp20250302_133047_586_25684
++ id -u
++ id -g
+ docker run --name pp20250302_133047_586_25684 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots R --vanilla
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("scaffolds.fasta.output.txt",header = TRUE,sep="\t",row.names=1); CairoPNG(file="scaffolds.fasta.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
null device
1
>
+ awk '-F\t' -v l=0.99 '{cnt[int($2)]+=$4; total+=$4; if(int($2)>max){max=int($2)}} END{for(i=1;i<=max;i++){print i"\t"cnt[i]+0; s+=cnt[i]; if(s>=total*l){print "over_"i"\t"total-s; break}}}'
+ tail -n+2 scaffolds.fasta.output.txt
+ echo 'library(Cairo); data=read.table("scaffolds.fasta.output.txt.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="scaffolds.fasta.output.txt.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()'
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots R --vanilla
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133048_719_7051
+ echo pp20250302_133048_719_7051
++ id -u
++ id -g
+ docker run --name pp20250302_133048_719_7051 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots R --vanilla
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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); data=read.table("scaffolds.fasta.output.txt.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="scaffolds.fasta.output.txt.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
null device
1
>
+ '[' true = true ']'
+ cat
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 bash run-makebam.sh "test_1.fq.sam" "16"'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 bash run-makebam.sh "test_2.fq.sam" "16"'
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
+ '[' true = true ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools merge scaffolds.fasta.bam test_1.fq.sam.clean.bam test_2.fq.sam.clean.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.19--h50ea8bc_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133052_895_24085
+ echo pp20250302_133052_895_24085
++ id -u
++ id -g
+ docker run --name pp20250302_133052_895_24085 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools merge scaffolds.fasta.bam test_1.fq.sam.clean.bam test_2.fq.sam.clean.bam
[bam_merge] File 'scaffolds.fasta.bam' exists. Please apply '-f' to overwrite. Abort.
PID: 2045302
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'post-assemble~coverage-length-graph_by-minimap2' -c 16 -m 32 -x true input_1/scaffolds.fasta input_2
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/post-assemble~coverage-length-graph_by-minimap2
Containers: c2997108/centos6:2-bwa-0.7.17-r1198-dirty c2997108/ubuntu20:R-2_gplots centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/samtools:1.19--h50ea8bc_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ ref=input_1/scaffolds.fasta
+ '[' '!' -e input_1/scaffolds.fasta.fai ']'
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ find input_2/ -maxdepth 1
++ egrep '[.]f(ast|)q(|[.]gz)$'
+ for i in `find $input_2/ -maxdepth 1 |egrep '[.]f(ast|)q(|[.]gz)$' || true`
++ basename input_2/test_1.fq
+ i2=test_1.fq
++ basename input_2/test_1.fq
++ sed 's/[.]f\(ast\|\)q.*//'
+ samplename=test_1
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -t 16 -ax map-ont '\''input_1/scaffolds.fasta'\'' '\''input_2/test_1.fq'\'' | ( PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -h -F 0x800 ) > '\''test_1.fq.sam'\'''
+ for i in `find $input_2/ -maxdepth 1 |egrep '[.]f(ast|)q(|[.]gz)$' || true`
++ basename input_2/test_2.fq
+ i2=test_2.fq
++ basename input_2/test_2.fq
++ sed 's/[.]f\(ast\|\)q.*//'
+ samplename=test_2
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -t 16 -ax map-ont '\''input_1/scaffolds.fasta'\'' '\''input_2/test_2.fq'\'' | ( PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -h -F 0x800 ) > '\''test_2.fq.sam'\'''
[M::mm_idx_gen::0.213*1.20] collected minimizers
[M::mm_idx_gen::0.302*1.97] sorted minimizers
[M::main::0.302*1.97] loaded/built the index for 2111 target sequence(s)
[M::mm_mapopt_update::0.325*1.90] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2111
[M::mm_idx_stat::0.342*1.85] distinct minimizers: 955730 (97.96% are singletons); average occurrences: 1.039; average spacing: 5.390; total length: 5354294
[M::worker_pipeline::0.464*3.05] mapped 10000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -t 16 -ax map-ont input_1/scaffolds.fasta input_2/test_1.fq
[M::main] Real time: 0.484 sec; CPU: 1.438 sec; Peak RSS: 0.066 GB
[M::mm_idx_gen::0.208*1.22] collected minimizers
[M::mm_idx_gen::0.261*2.36] sorted minimizers
[M::main::0.261*2.36] loaded/built the index for 2111 target sequence(s)
[M::mm_mapopt_update::0.292*2.21] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2111
[M::mm_idx_stat::0.308*2.15] distinct minimizers: 955730 (97.96% are singletons); average occurrences: 1.039; average spacing: 5.390; total length: 5354294
[M::worker_pipeline::0.442*3.29] mapped 10000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -t 16 -ax map-ont input_1/scaffolds.fasta input_2/test_2.fq
[M::main] Real time: 0.461 sec; CPU: 1.473 sec; Peak RSS: 0.064 GB
+ cat
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots bash run-cleanup.sh "test_1.fq.sam" "0.3" "0" "input_1/scaffolds.fasta"'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots bash run-cleanup.sh "test_2.fq.sam" "0.3" "0" "input_1/scaffolds.fasta"'
+ xargs '-d\n' -I '{}' -P 16 bash -c '{}'
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("test_1.fq.sam2.cov",sep="\t",row.names=1);
> CairoPNG(file="test_1.fq.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
> library(Cairo); a=read.table("test_2.fq.sam2.cov",sep="\t",row.names=1);
> CairoPNG(file="test_2.fq.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
Error in rep.int(i.multi, number[number > 1]) : invalid 'times' value
Calls: sunflowerplot -> sunflowerplot.default
Execution halted
Error in rep.int(i.multi, number[number > 1]) : invalid 'times' value
Calls: sunflowerplot -> sunflowerplot.default
Execution halted
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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); data=read.table("test_1.fq.sam2.cov.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="test_1.fq.sam2.cov.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
> library(Cairo); data=read.table("test_2.fq.sam2.cov.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="test_2.fq.sam2.cov.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
null device
1
>
null device
1
>
++ basename input_1/scaffolds.fasta
+ outname=scaffolds.fasta
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME!=ARGV[1]{bases[$1]+=$3} END{print "id\tcoverage\tmapped bases\tlength"; for(i in len){if(bases[i]>0){print i"\t"bases[i]/len[i]"\t"bases[i]+0"\t"len[i]}}}' input_1/scaffolds.fasta.fai test_1.fq.sam2.cov test_2.fq.sam2.cov
+ echo 'library(Cairo); a=read.table("scaffolds.fasta.output.txt",header = TRUE,sep="\t",row.names=1); CairoPNG(file="scaffolds.fasta.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()'
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots R --vanilla
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133119_520_25717
+ echo pp20250302_133119_520_25717
++ id -u
++ id -g
+ docker run --name pp20250302_133119_520_25717 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots R --vanilla
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("scaffolds.fasta.output.txt",header = TRUE,sep="\t",row.names=1); CairoPNG(file="scaffolds.fasta.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
null device
1
>
+ tail -n+2 scaffolds.fasta.output.txt
+ awk '-F\t' -v l=0.99 '{cnt[int($2)]+=$4; total+=$4; if(int($2)>max){max=int($2)}} END{for(i=1;i<=max;i++){print i"\t"cnt[i]+0; s+=cnt[i]; if(s>=total*l){print "over_"i"\t"total-s; break}}}'
+ echo 'library(Cairo); data=read.table("scaffolds.fasta.output.txt.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="scaffolds.fasta.output.txt.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()'
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots R --vanilla
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133120_660_2418
+ echo pp20250302_133120_660_2418
++ id -u
++ id -g
+ docker run --name pp20250302_133120_660_2418 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots R --vanilla
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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); data=read.table("scaffolds.fasta.output.txt.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="scaffolds.fasta.output.txt.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
null device
1
>
+ '[' true = true ']'
+ cat
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 bash run-makebam.sh "test_1.fq.sam" "16"'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 bash run-makebam.sh "test_2.fq.sam" "16"'
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
+ '[' true = true ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools merge -f scaffolds.fasta.bam test_1.fq.sam.clean.bam test_2.fq.sam.clean.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.19--h50ea8bc_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133125_006_195
+ echo pp20250302_133125_006_195
++ id -u
++ id -g
+ docker run --name pp20250302_133125_006_195 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools merge -f scaffolds.fasta.bam test_1.fq.sam.clean.bam test_2.fq.sam.clean.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools index scaffolds.fasta.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.19--h50ea8bc_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133126_187_22693
+ echo pp20250302_133126_187_22693
++ id -u
++ id -g
+ docker run --name pp20250302_133126_187_22693 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools index scaffolds.fasta.bam
+ rm -f test_1.fq.sam test_2.fq.sam test_1.fq.sam2 test_2.fq.sam2
+ awk '{a+=$5} END{print a}'
+ sed s/,//g
+ tail -n+2
++ egrep '[.]f(ast|)q(|[.]gz)$'
++ find input_2 -maxdepth 1
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:0.12.1--0 seqkit stats input_2/test_1.fq input_2/test_2.fq
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:0.12.1--0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_133127_313_19626
+ echo pp20250302_133127_313_19626
++ id -u
++ id -g
+ docker run --name pp20250302_133127_313_19626 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit stats input_2/test_1.fq input_2/test_2.fq
+ awk -v n=20 'NR<=n{a+=$2} END{print a/n}'
+ sort -k4,4nr -t ' '
+ tail -n+2 scaffolds.fasta.output.txt
++ cat temp.txt
++ cat temp2.txt
+ awk -v total=2000000 -v depth=0.231009 -v n=20 'BEGIN{print "Total bases of input reads: "total" bp"; print "Average depth of the longest "n" contigs: "depth" x"; print "Estimated genome size: "total / depth" bp"}'
+ rm -f temp.txt temp2.txt
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 2231775
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'post-assemble~coverage-length-graph_by-minimap2' -c 16 -m 32 -x true input_1/scaffolds.fasta input_2
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/post-assemble~coverage-length-graph_by-minimap2
Containers: c2997108/centos6:2-bwa-0.7.17-r1198-dirty c2997108/ubuntu20:R-2_gplots centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/samtools:1.19--h50ea8bc_0 quay.io/biocontainers/seqkit:0.12.1--0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ ref=input_1/scaffolds.fasta
+ '[' '!' -e input_1/scaffolds.fasta.fai ']'
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ find input_2/ -maxdepth 1
++ egrep '[.]f(ast|)q(|[.]gz)$'
+ for i in `find $input_2/ -maxdepth 1 |egrep '[.]f(ast|)q(|[.]gz)$' || true`
++ basename input_2/test_1.fq
+ i2=test_1.fq
++ basename input_2/test_1.fq
++ sed 's/[.]f\(ast\|\)q.*//'
+ samplename=test_1
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -t 16 -ax map-ont '\''input_1/scaffolds.fasta'\'' '\''input_2/test_1.fq'\'' | ( PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -h -F 0x900 ) > '\''test_1.fq.sam'\'''
+ for i in `find $input_2/ -maxdepth 1 |egrep '[.]f(ast|)q(|[.]gz)$' || true`
++ basename input_2/test_2.fq
+ i2=test_2.fq
++ basename input_2/test_2.fq
++ sed 's/[.]f\(ast\|\)q.*//'
+ samplename=test_2
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -t 16 -ax map-ont '\''input_1/scaffolds.fasta'\'' '\''input_2/test_2.fq'\'' | ( PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -h -F 0x900 ) > '\''test_2.fq.sam'\'''
[M::mm_idx_gen::0.217*1.10] collected minimizers
[M::mm_idx_gen::0.303*1.53] sorted minimizers
[M::main::0.303*1.52] loaded/built the index for 2111 target sequence(s)
[M::mm_mapopt_update::0.323*1.49] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2111
[M::mm_idx_stat::0.338*1.47] distinct minimizers: 955730 (97.96% are singletons); average occurrences: 1.039; average spacing: 5.390; total length: 5354294
[M::worker_pipeline::0.487*2.70] mapped 10000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -t 16 -ax map-ont input_1/scaffolds.fasta input_2/test_1.fq
[M::main] Real time: 0.504 sec; CPU: 1.333 sec; Peak RSS: 0.075 GB
[M::mm_idx_gen::0.282*1.07] collected minimizers
[M::mm_idx_gen::0.329*1.89] sorted minimizers
[M::main::0.329*1.89] loaded/built the index for 2111 target sequence(s)
[M::mm_mapopt_update::0.351*1.83] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2111
[M::mm_idx_stat::0.370*1.79] distinct minimizers: 955730 (97.96% are singletons); average occurrences: 1.039; average spacing: 5.390; total length: 5354294
[M::worker_pipeline::0.515*2.90] mapped 10000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -t 16 -ax map-ont input_1/scaffolds.fasta input_2/test_2.fq
[M::main] Real time: 0.529 sec; CPU: 1.508 sec; Peak RSS: 0.067 GB
+ cat
+ for i in *.sam
+ xargs '-d\n' -I '{}' -P 16 bash -c '{}'
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots bash run-cleanup.sh "test_1.fq.sam" "0.3" "0" "input_1/scaffolds.fasta"'
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots bash run-cleanup.sh "test_2.fq.sam" "0.3" "0" "input_1/scaffolds.fasta"'
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("test_1.fq.sam2.cov",sep="\t",row.names=1);
> CairoPNG(file="test_1.fq.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
> library(Cairo); a=read.table("test_2.fq.sam2.cov",sep="\t",row.names=1);
> CairoPNG(file="test_2.fq.sam2.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
Error in rep.int(i.multi, number[number > 1]) : invalid 'times' value
Calls: sunflowerplot -> sunflowerplot.default
Execution halted
Error in rep.int(i.multi, number[number > 1]) : invalid 'times' value
Calls: sunflowerplot -> sunflowerplot.default
Execution halted
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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); data=read.table("test_1.fq.sam2.cov.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="test_1.fq.sam2.cov.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
> library(Cairo); data=read.table("test_2.fq.sam2.cov.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="test_2.fq.sam2.cov.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
null device
1
>
null device
1
>
++ basename input_1/scaffolds.fasta
+ outname=scaffolds.fasta
+ awk '-F\t' 'FILENAME==ARGV[1]{len[$1]=$2} FILENAME!=ARGV[1]{bases[$1]+=$3} END{print "id\tcoverage\tmapped bases\tlength"; for(i in len){if(bases[i]>0){print i"\t"bases[i]/len[i]"\t"bases[i]+0"\t"len[i]}}}' input_1/scaffolds.fasta.fai test_1.fq.sam2.cov test_2.fq.sam2.cov
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots R --vanilla
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ echo 'library(Cairo); a=read.table("scaffolds.fasta.output.txt",header = TRUE,sep="\t",row.names=1); CairoPNG(file="scaffolds.fasta.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()'
+ PPDOCNAME=pp20250302_170037_711_1102
+ echo pp20250302_170037_711_1102
++ id -u
++ id -g
+ docker run --name pp20250302_170037_711_1102 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots R --vanilla
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("scaffolds.fasta.output.txt",header = TRUE,sep="\t",row.names=1); CairoPNG(file="scaffolds.fasta.cov.png",width=1000,height=1000); sunflowerplot(x=a[,1], y=a[,3], xlab="coverage [fold]", ylab="contig length [bp]", log="xy"); dev.off()
null device
1
>
+ awk '-F\t' -v l=0.99 '{cnt[int($2)]+=$4; total+=$4; if(int($2)>max){max=int($2)}} END{for(i=1;i<=max;i++){print i"\t"cnt[i]+0; s+=cnt[i]; if(s>=total*l){print "over_"i"\t"total-s; break}}}'
+ tail -n+2 scaffolds.fasta.output.txt
+ echo 'library(Cairo); data=read.table("scaffolds.fasta.output.txt.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="scaffolds.fasta.output.txt.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()'
+ FUNC_RUN_DOCKER c2997108/ubuntu20:R-2_gplots R --vanilla
+ PP_RUN_IMAGE=c2997108/ubuntu20:R-2_gplots
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_170038_844_15608
+ echo pp20250302_170038_844_15608
++ id -u
++ id -g
+ docker run --name pp20250302_170038_844_15608 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/ubuntu20:R-2_gplots R --vanilla
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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); data=read.table("scaffolds.fasta.output.txt.hist",sep="\t", header = FALSE);colnames(data) <- c("Coverage", "Frequency"); CairoPNG(file="scaffolds.fasta.output.txt.hist.png",width=1000,height=1000); plot(data$Coverage, data$Frequency, type = "o", col = "blue", main = "Coverage Histogram", xlab = "Depth", ylab = "Total bases of contigs"); dev.off()
null device
1
>
+ '[' true = true ']'
+ cat
+ for i in *.sam
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 bash run-makebam.sh "test_1.fq.sam" "16"'
+ for i in *.sam
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 bash run-makebam.sh "test_2.fq.sam" "16"'
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
+ '[' true = true ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools merge -f scaffolds.fasta.bam test_1.fq.sam.clean.bam test_2.fq.sam.clean.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.19--h50ea8bc_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_170042_655_7513
+ echo pp20250302_170042_655_7513
++ id -u
++ id -g
+ docker run --name pp20250302_170042_655_7513 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools merge -f scaffolds.fasta.bam test_1.fq.sam.clean.bam test_2.fq.sam.clean.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools index scaffolds.fasta.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.19--h50ea8bc_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_170043_842_11892
+ echo pp20250302_170043_842_11892
++ id -u
++ id -g
+ docker run --name pp20250302_170043_842_11892 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools index scaffolds.fasta.bam
+ rm -f test_1.fq.sam test_2.fq.sam test_1.fq.sam2 test_2.fq.sam2
+ tail -n+2
+ awk '{a+=$5} END{print a}'
+ sed s/,//g
++ find input_2 -maxdepth 1
++ egrep '[.]f(ast|)q(|[.]gz)$'
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:0.12.1--0 seqkit stats input_2/test_1.fq input_2/test_2.fq
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:0.12.1--0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250302_170044_760_11789
+ echo pp20250302_170044_760_11789
++ id -u
++ id -g
+ docker run --name pp20250302_170044_760_11789 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2 -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:0.12.1--0 seqkit stats input_2/test_1.fq input_2/test_2.fq
+ tail -n+2 scaffolds.fasta.output.txt
+ sort -k4,4nr -t ' '
+ awk -v n=20 'NR<=n{a+=$2} END{print a/n}'
++ cat temp.txt
++ cat temp2.txt
+ awk -v total=2000000 -v depth=0.227699 -v n=20 'BEGIN{print "Total bases of input reads: "total" bp"; print "Average depth of the longest "n" contigs: "depth" x"; print "Estimated genome size: "total / depth" bp"}'
+ rm -f temp.txt temp2.txt
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/post-assemble~coverage-length-graph_by-minimap2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit