assemble~oatk

An organelle genome assembly toolkit for HiFi reads. By including the genome file as input, a FASTA file is generated in which incomplete organelle genomes are removed and complete organelle genomes are added.

input_1:HiFi reads (FASTQ)

input_1/ch.fastq

@cbba8101-681a-4320-9d61-c3555dc46ca7	qs:f:25.3335	st:Z:2025-03-05T09:33:25.314+00:00	RG:Z:9a437f06beab108e7b38c9f080a4b387fa2444d6_dna_r10.4.1_e8.2_400bps_sup@v5.0.0
CTATCATCCATGTTACAAACTATGCGAACGTCAAAAGGTCTTACAACCGAACAAGCTACAAAACTACTAACATACAATATTCAGAATGACAACTTATCAAAAGAACGCAAAGAATTCCTAATGAAAAAAGCAATATGGATATTCTATACAAATGCAAAGGTTGATACACACAATTTCACCATGATGAAATCAATTGTAAATGAAAAAAATCCTGTATGCAATTGTATGGGATACTTTAGTCCAGCACAAGGAAGTAACAGAGAAGTAGGAAACAGAACACATTTTGCATATTCAGAGCTGAAAAAAATTAATTCCACCATATGTCGGGGAGCAAGAGTAGCACTTGACAGAAACATCTGGGATAACATAGGCCTTTATAATGGCGCAATGGGGACTGTAATTGATATCCGTTTTGAACATAAAAAGAACCCTTTACAAGGAGACCTACCAAAATATGTAATTGTTGACTTTGACGAATATAAAGGACCACCTTGGAATGAATCAAATCCGTCCTACCTACCAATTCCACCATGTACAATACGATGCCGTAATGGATGCTGTACTTTCACAAAAATCCCTTTGACACTTTCTTGGGCAAGAACAGCACATAAATTTCAAGGTTCCAATGTTGGAAGTACATATCCAATCAAAGCAATGGTATTTGACCCTGGACAAACTGGTGTAGAAGGAAACAACCCAGGCTTTACATACGTTGGTTTAAGTAGAGTTTCCTCACTGGGACAAGGTAAAATTGAAAAATCTGCCCTTTACTTGACTGGTGAGAACCTCACCATGGAAAGATTCACTGATATGACATATCAAAGAACTAGAAAAAATGAAATGTACGTCAAAGTACAGGAGAAACAGATGGATACTACATCTACTACGACAAAAAACAAGAACAAACCTTGCAATCACACCAGACACCAAGACAAATTTAAAACGCTGGACACAGACAAATACTTATACTACTCTTCAACTAGAGCAAGCCATATTGTTCCATTCAGAACATTAAAACAACTCAGAGAAATATCATGATGGGTAAGATTCTATTTAGAATCTGACACATACACACTTCTATCTATTTGAGTGAAATTCTGTTCAGAAGTTCACACATAACTCTAATAACCTTTACTAAACTATTTACAATAATATACAACTTCTCATAAATTACTCTTTTACTTTTAACCTTTCAATCATTATTTCACAACTACACTTTCCTATCACGTGGTGACAACATATTCCCTAAGTACATGCATTTCAGACAATCCCCCACGCGCAGATTTACAATCTTAACATTCTTTCATAAATATAATGGTAGTCTCAACAAGAACTTCTGGTAAAAAAGCTTCAAAAAGATCCTCATCTTTTGTTCGGCAGCCCAAAAATGTCAGAACCAACAGATTTCAAAGGATACCATCCAGCCAACATAACCTCAACATGCCCCCCCAGTCAATAACAGAAGTGTTCCGGACTCAAATGAAAATAGGCTGGATATTGATTTAAAAAAAAAAAACTAATTTGTGATCACTGCAAGTTGGGATTTGATACAAAAAAAGAATTTTATTGCGCACACAACGACCTCACCGGCATGCAAGTATGTGCTGGGCTATTGTTATGGATGCAAGTCTACCTTCACCTCACAAAAAGCACTTACCCAACATTTAAATCACTCCAGTAAACAAGAATGTGGTGTCAAGCATATTTCCAATATGTTGGAATTTGCAACGACCTCCACTATGCCTATTGCCTTGGAGACAAACCAACAAACACAAATTTTGGTGAATCAGAAAGATTTGGCCCTTCACAACCTAAATAAAACCGCCACCAACAATAGACTCATAATGCAATCTATGCAATCCCAACTTCCTGGCACCTTTAATTATCCTGGTATTATGCAAAATTCTGGAGAATTTAACAATCATTATGATCACGACACCTCACAAGACAATTTTGATTTTTCTTCCCATGCACAATTTCCATCTTCTGTTGAAGATAACATTGACTTTATCAGCAATAACGGAGATGATGTCGAACATGAAATACCACGAGAAAACATAACTCCTCCATCCAATTCCTATTTATTCAAGCGAATGATTAGACAGAAAGAAAAAATTGAAGTAATACGGGATCAAGTCACTTGGAGCAACCAAATAACAGCAGCTCTTGAACTCGAACAGATTCTCCACAAGTCAGGAGCTCCATTGGGTCTCTTTTATAAGGTTATGGCCTGGGCTACAGAGAATCAGACATCCTTACCAGAACGAACGCTTCAACTTTCCCGCACACGCTTGTACAATACCTGTAGGGAGAAAATGTATGGCTGTGATCATGAGAAAAAACCGGAATTCAAGGTTTCTGCTAACCCACCTAAAATAGTGTCGGTCAAATTACCGTCCAAGAGAACTATCAATGTTGCCACATTCAGTTTTTTAGAACATCTGACCAGCATGCTATCCAGCAAAGAGCTTATGGCTGAAGAGAATCTAATATTTGAGAGGAAACCTAATGATCCTTTTCACGTACCGAGGGATAATGAAAGATATGGAGATGTCCATCAATGTAAATATTGGGATGACACTGTCGACATGCTCATCAATGATCCAACAACCGAAATTTTATGCCCCCTTATTCTTTATCTTGATGCCCTGGTTGTGGATGCATACGGAAATTTATCCCTTGAACCTGTAACATTTACGCTTGGCATTTTCAAGCGACTCCTTAGACATCATGGAAAAGCATGGAGAACTCTTGGATTCATAGAGGACCTGGATAGTCTATTCGGTGCCAACCATATCAAGCCATTGCAGAAAGCCAATGATTACCATGCAAT

input_2:An assembled genome file

input_2/ont-ds-telo-contigs.bp.p_ctg.fa

>ptg000001l
TGAAGAATATGTTACCATGATACAGATCCCTAACTTTAGGACAGTATTTACTCTTGATGACACAAACATTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGACCATGTACCTGGGGTGACCCCCCGTGAAATTTTGATTTTCTTTAAGATTCTTGTAGAGCATCCCAAGGGCTACAAAATGTGCGTAGGTCCCAGCTCAAAACTCGCAATAGCCTTAGATATGGTCATTTTGCTACTACTAGTGGGAAGCTAGTAATTTTGACTTTTATTTCAGTTAAGGTCAAGTATCTCAAAACTGTACGTTGGTCCCGAGCTGAAACTTCAGCACAAGAAAAATGGCGATAAGGGCTAACTTTTGACACCCCAACGACTAATTTAGCTGCCATATTTTTTATTTTTTCAAAATCTTGCATTTTTTTATTTCTCTGATTACCACCACTTTCAATGAAATTTTGAAAAAAATATCATGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTCATGAACGTGTAGATATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACTGTGCTACTACCACATACCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACATGATCGAATGTACATGATATATGATATACCTTCCTGGAATGATGACCCCACATTGGCAAGGTTATGAACGTGTAGATATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACCATACTACTACCACATAACACCACATTGACTTTTTTCAACCAAATTTTCATATCAACATGATCAAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTTATGAACGTGTAGATATTCACTATTCATTGCTATCTACTAGCTTTCAACTAGTGAACACTGTGCTACTACCACATACCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAACGTCATGAACGTGTAGTTATTCACTATTCATTACTATCTACTAGCTTTCAACTAGTGAACACTATACTACTACCACATACCATCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTCATGAACGTGTAGATATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACTGTGCTACTACCACATACCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACATGATCGAATGTACATGATATATGATATTCTTGGCTGGAATCATGACCCCACATTGGCAAGGTTATGAACGTGTAGATATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACCATACTACTACCACATAACACCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTTATGAACGTGTAGATATTCACTATTCATTGCTATCTACTAGCTTTCAACTAGTGAACACTGTGCTACTACCACATACCATCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTTATGAACGTGTAGATATTCACTATTCATTGCTATCTACTAGCTTTCAACTAGTGAACACTATGCTACTACCACATACCATCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAACGTCATGAACGTGTAGTTATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACTATACTACTACCACATACCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAACGTCATGAACGTGTAGTTATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACTATACTACTACCACATGCCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAACGTCATGAACGTGTAGATATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACTATACTACTACCACATGCCACCATATGGACTTTTTTCAACCAAATTTTCATATCAACGTGATTGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAACGTCATGAACGTGTAGATATTCACTATTCATTGCTATCTACTAGCTTTCAACTAGTAAACACTATGCTACTACCACATACCATCACATTGACCTTTTTCAACCAAAATTTTCATATCAACATGATCAAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTCATGAATGTGTAGTTATTCACTATTCATTACTATCTACTAGCTTTCAACTAGCGAACACTATGCTACTACCACATAACACCACATTGACTTTTTTCTACCAAATTTGCATATCAACATGATCGAATGTACATGATATATGATATTCTTGGCTGGAATCATGACCCCACATTGGCAAGGTCATGAATGTGTAGTTATTCACTATTCATTACTATCTACTAGCTTTCAACTAGTGAACACTATGCTACTACCACATACCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACATGATC

input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa

>ptg000001l
TGAAGAATATGTTACCATGATACAGATCCCTAACTTTAGGACAGTATTTACTCTTGATGACACAAACATTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGACCATGTACCTGGGGTGACCCCCCGTGAAATTTTGATTTTCTTTAAGATTCTTGTAGAGCATCCCAAGGGCTACAAAATGTGCGTAGGTCCCAGCTCAAAACTCGCAATAGCCTTAGATATGGTCATTTTGCTACTACTAGTGGGAAGCTAGTAATTTTGACTTTTATTTCAGTTAAGGTCAAGTATCTCAAAACTGTACGTTGGTCCCGAGCTGAAACTTCAGCACAAGAAAAATGGCGATAAGGGCTAACTTTTGACACCCCAACGACTAATTTAGCTGCCATATTTTTTATTTTTTCAAAATCTTGCATTTTTTTATTTCTCTGATTACCACCACTTTCAATGAAATTTTGAAAAAAATATCATGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTCATGAACGTGTAGATATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACTGTGCTACTACCACATACCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACATGATCGAATGTACATGATATATGATATACCTTCCTGGAATGATGACCCCACATTGGCAAGGTTATGAACGTGTAGATATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACCATACTACTACCACATAACACCACATTGACTTTTTTCAACCAAATTTTCATATCAACATGATCAAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTTATGAACGTGTAGATATTCACTATTCATTGCTATCTACTAGCTTTCAACTAGTGAACACTGTGCTACTACCACATACCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAACGTCATGAACGTGTAGTTATTCACTATTCATTACTATCTACTAGCTTTCAACTAGTGAACACTATACTACTACCACATACCATCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTCATGAACGTGTAGATATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACTGTGCTACTACCACATACCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACATGATCGAATGTACATGATATATGATATTCTTGGCTGGAATCATGACCCCACATTGGCAAGGTTATGAACGTGTAGATATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACCATACTACTACCACATAACACCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTTATGAACGTGTAGATATTCACTATTCATTGCTATCTACTAGCTTTCAACTAGTGAACACTGTGCTACTACCACATACCATCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTTATGAACGTGTAGATATTCACTATTCATTGCTATCTACTAGCTTTCAACTAGTGAACACTATGCTACTACCACATACCATCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAACGTCATGAACGTGTAGTTATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACTATACTACTACCACATACCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAACGTCATGAACGTGTAGTTATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACTATACTACTACCACATGCCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACGTGATCGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAACGTCATGAACGTGTAGATATTCACTATTCGTTACTATCTACTAGCTTTCAACTAGTGAACACTATACTACTACCACATGCCACCATATGGACTTTTTTCAACCAAATTTTCATATCAACGTGATTGAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAACGTCATGAACGTGTAGATATTCACTATTCATTGCTATCTACTAGCTTTCAACTAGTAAACACTATGCTACTACCACATACCATCACATTGACCTTTTTCAACCAAAATTTTCATATCAACATGATCAAATGTACATGATATATGATATACCTTCCTGGAATCATGACCCCACATTGGCAAGGTCATGAATGTGTAGTTATTCACTATTCATTACTATCTACTAGCTTTCAACTAGCGAACACTATGCTACTACCACATAACACCACATTGACTTTTTTCTACCAAATTTGCATATCAACATGATCGAATGTACATGATATATGATATTCTTGGCTGGAATCATGACCCCACATTGGCAAGGTCATGAATGTGTAGTTATTCACTATTCATTACTATCTACTAGCTTTCAACTAGTGAACACTATGCTACTACCACATACCACCACATTGACTTTTTTCAACCAAATTTTCATATCAACATGATC

Command

assemble~oatk -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa -m embryophyta_mito.fam -p embryophyta_pltd.fam input_1/

Output

oatk.asm.pltd.ctg.fasta

>ctg000001c	length=117617 wlength=29044843.0 nv=4 circular=true path=u4-,u2-,u3+,u2+
TGAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCATATCCGGTG
TAGGCGTTAGAATATTGAGAGGAGCCTTCTTTAGTACGAGAGGACCGAGAAGGACATACC
TATGGTGTACCAGTTATCGTGCCAACGGTAAACGCTGGGTAGCTAAGTATGGAGTGGATA
ACCGCTGAAAGCATCTAAGTGGGAAGCCCACCTCAAGATGAGTATTCTCATCACGAAAGT
GAGTAAGGTCACGGTAAGACTAACCGTTTAATAGGCATCAAGTGTAAGTACAGTAATGTA
TGTGCTGAGATGTCCTAACAGACCGAGGACTTGAATTTTTAAAAGATATTTTTAAGAAAT
AGTTTCTTAAAAATATCACATATCTTTAAAGTAATTTTACTTTAAAGATTTTTGCTTTGG
TGTTTCTAGTGTACTGAACGGACCCACGCTGATCCATCTCGAACTCAGCTGTGAAACGTT
ATAAATCGGTGACAATACTTGGGGGGAGACCTCCTGGGAAGATAGCTCAATGCCAAAGTT

view all outputs

Log

pp assemble~oatk -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa input_1/
PID: 135793
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'assemble~oatk' -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa input_1/
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk
Containers: c2997108/oatk:1.0 centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ input_hifi=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' '' = '' ']'
+ input_hifi=input_1//ch.fastq
+ read i
+ echo HiFi reads: input_1//ch.fastq
HiFi reads: input_1//ch.fastq
+ optpltd=
+ '[' '' '!=' '' ']'
/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk: 行 42: t: 未割り当ての変数です

PID: 138151
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'assemble~oatk' -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa input_1/
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk
Containers: c2997108/oatk:1.0 centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ input_hifi=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' '' = '' ']'
+ input_hifi=input_1//ch.fastq
+ read i
+ echo HiFi reads: input_1//ch.fastq
HiFi reads: input_1//ch.fastq
+ optpltd=
+ '[' '' '!=' '' ']'
/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk: 行 42: t: 未割り当ての変数です

PID: 139644
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'assemble~oatk' -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa -t dikarya_mito.fam input_1/
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk
Containers: c2997108/oatk:1.0 centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ input_hifi=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' '' = '' ']'
+ input_hifi=input_1//ch.fastq
+ read i
+ echo HiFi reads: input_1//ch.fastq
HiFi reads: input_1//ch.fastq
+ optpltd=
+ '[' '' '!=' '' ']'
/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk: 行 42: t: 未割り当ての変数です

PID: 141589
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'assemble~oatk' -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa input_1/
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk
Containers: c2997108/oatk:1.0 centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ input_hifi=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' '' = '' ']'
+ input_hifi=input_1//ch.fastq
+ read i
+ echo HiFi reads: input_1//ch.fastq
HiFi reads: input_1//ch.fastq
+ optpltd=
+ '[' '' '!=' '' ']'
+ FUNC_RUN_DOCKER c2997108/oatk:1.0 oatk -o oatk.asm -t 8 -t /usr/local/oatkdb/dikarya_mito.fam input_1//ch.fastq
+ PP_RUN_IMAGE=c2997108/oatk:1.0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_014514_230_8018
+ echo pp20250515_014514_230_8018
++ id -u
++ id -g
+ docker run --name pp20250515_014514_230_8018 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/oatk:1.0 oatk -o oatk.asm -t 8 -t /usr/local/oatkdb/dikarya_mito.fam input_1//ch.fastq
[E::main] provide at least one HMM profile database (-m and/or -p)

PID: 142694
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'assemble~oatk' -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa input_1/
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk
Containers: c2997108/oatk:1.0 centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ input_hifi=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' '' = '' ']'
+ input_hifi=input_1//ch.fastq
+ read i
+ echo HiFi reads: input_1//ch.fastq
HiFi reads: input_1//ch.fastq
+ optpltd=
+ '[' '' '!=' '' ']'
+ FUNC_RUN_DOCKER c2997108/oatk:1.0 oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam input_1//ch.fastq
+ PP_RUN_IMAGE=c2997108/oatk:1.0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_014601_053_11569
+ echo pp20250515_014601_053_11569
++ id -u
++ id -g
+ docker run --name pp20250515_014601_053_11569 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/oatk:1.0 oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam input_1//ch.fastq
[M::syncasm] collected syncmers from 100000 target sequence(s)
[M::sr_db_stat] number syncmers collected: 612053
[M::sr_db_stat] number syncmers per read: 6.121
[M::sr_db_stat] average kmer space: -619.665
[M::sr_db_stat] number uniqe smer: 203238; singletons: 125029 (61.519%)
[M::sr_db_stat] average smer count: 3.012
[M::sr_db_stat] smer peak_hom: 22; peak_het: -1
[M::sr_db_stat] number uniqe kmer: 491420; singletons: 458727 (93.347%)
[M::sr_db_stat] average kmer count: 1.245
[M::sr_db_stat] kmer peak_hom: 15; peak_het: 11
[M::find_error_syncmers] error syncmer candidates: num = 491361, max_c = 83
[M::read_error_correction] Error Correction Summary Results
[M::read_error_correction] total number of error blocks : 2275
[M::read_error_correction]                - uncorrected : 2157
[M::read_error_correction]                  - corrected : 97
[M::read_error_correction]             - ambiguous seqs : 0
[M::read_error_correction]             - ambiguous path : 0
[M::sr_db_stat] number syncmers collected: 617240
[M::sr_db_stat] number syncmers per read: 6.172
[M::sr_db_stat] average kmer space: -619.567
[M::sr_db_stat] number uniqe smer: 203213; singletons: 125017 (61.520%)
[M::sr_db_stat] average smer count: 3.037
[M::sr_db_stat] smer peak_hom: 22; peak_het: -1
[M::sr_db_stat] number uniqe kmer: 491367; singletons: 458685 (93.349%)
[M::sr_db_stat] average kmer count: 1.256
[M::sr_db_stat] kmer peak_hom: 15; peak_het: 11
[M::syncasm] make syncmer graph
[M::syncasm] syncmer graph stats
[M::scg_stat] number unitigs  : 178
[M::scg_stat] number syncmers : 178
[M::scg_stat] number arcs     : 314
[M::syncasm] syncmer graph unitigging
[M::syncasm] syncmer graph stats after unitigging
[M::scg_stat] number unitigs  : 35
[M::scg_stat] number syncmers : 178
[M::scg_stat] number arcs     : 28
[M::syncasm] syncmer graph cleanup
[M::syncasm] assembly graph unzipping
[M::scg_read_alignment] 65248 mappable reads, 429 mapped (429 unique mapping)
[M::scg_read_alignment] 65248 mappable reads, 85 mapped (85 unique mapping)
[M::scg_read_alignment] 65248 mappable reads, 429 mapped (429 unique mapping)
[M::scg_read_alignment] 65248 mappable reads, 429 mapped (429 unique mapping)
[M::syncasm] syncmer graph stats after final processing
[M::scg_stat] number unitigs  : 18
[M::scg_stat] number syncmers : 113
[M::scg_stat] number arcs     : 28
[M::annot_worker_pipeline] 18 sequences (86446 bp) loaded in 1 batch
[W::gfa_parse_L] the coverage of arc 'u7-' -> 'u7-' is zero
[W::gfa_parse_L] the coverage of arc 'u7+' -> 'u7+' is zero
[W::gfa_parse_L] the coverage of arc 'u13-' -> 'u13-' is zero
[W::gfa_parse_L] the coverage of arc 'u13+' -> 'u13+' is zero
[M::main] Version: 1.0
[M::main] CMD: oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam input_1//ch.fastq
[M::main] Real time: 57.733 sec; CPU: 18.331 sec; Peak RSS: 1.129 GB
/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk: 行 71: 予期しないトークン `(' 周辺に構文エラーがあります

PID: 144467
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'assemble~oatk' -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa input_1/
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk
Containers: c2997108/oatk:1.0 centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ input_hifi=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' '' = '' ']'
+ input_hifi=input_1//ch.fastq
+ read i
+ echo HiFi reads: input_1//ch.fastq
HiFi reads: input_1//ch.fastq
+ optpltd=
+ '[' '' '!=' '' ']'
+ FUNC_RUN_DOCKER c2997108/oatk:1.0 oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam input_1//ch.fastq
+ PP_RUN_IMAGE=c2997108/oatk:1.0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_014742_214_29201
+ echo pp20250515_014742_214_29201
++ id -u
++ id -g
+ docker run --name pp20250515_014742_214_29201 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/oatk:1.0 oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam input_1//ch.fastq
[M::syncasm] collected syncmers from 100000 target sequence(s)
[M::sr_db_stat] number syncmers collected: 612053
[M::sr_db_stat] number syncmers per read: 6.121
[M::sr_db_stat] average kmer space: -619.665
[M::sr_db_stat] number uniqe smer: 203238; singletons: 125029 (61.519%)
[M::sr_db_stat] average smer count: 3.012
[M::sr_db_stat] smer peak_hom: 22; peak_het: -1
[M::sr_db_stat] number uniqe kmer: 491420; singletons: 458727 (93.347%)
[M::sr_db_stat] average kmer count: 1.245
[M::sr_db_stat] kmer peak_hom: 15; peak_het: 11
[M::find_error_syncmers] error syncmer candidates: num = 491361, max_c = 83
[M::read_error_correction] Error Correction Summary Results
[M::read_error_correction] total number of error blocks : 2275
[M::read_error_correction]                - uncorrected : 2157
[M::read_error_correction]                  - corrected : 97
[M::read_error_correction]             - ambiguous seqs : 0
[M::read_error_correction]             - ambiguous path : 0
[M::sr_db_stat] number syncmers collected: 617240
[M::sr_db_stat] number syncmers per read: 6.172
[M::sr_db_stat] average kmer space: -619.567
[M::sr_db_stat] number uniqe smer: 203213; singletons: 125017 (61.520%)
[M::sr_db_stat] average smer count: 3.037
[M::sr_db_stat] smer peak_hom: 22; peak_het: -1
[M::sr_db_stat] number uniqe kmer: 491367; singletons: 458685 (93.349%)
[M::sr_db_stat] average kmer count: 1.256
[M::sr_db_stat] kmer peak_hom: 15; peak_het: 11
[M::syncasm] make syncmer graph
[M::syncasm] syncmer graph stats
[M::scg_stat] number unitigs  : 178
[M::scg_stat] number syncmers : 178
[M::scg_stat] number arcs     : 314
[M::syncasm] syncmer graph unitigging
[M::syncasm] syncmer graph stats after unitigging
[M::scg_stat] number unitigs  : 35
[M::scg_stat] number syncmers : 178
[M::scg_stat] number arcs     : 28
[M::syncasm] syncmer graph cleanup
[M::syncasm] assembly graph unzipping
[M::scg_read_alignment] 65248 mappable reads, 429 mapped (429 unique mapping)
[M::scg_read_alignment] 65248 mappable reads, 85 mapped (85 unique mapping)
[M::scg_read_alignment] 65248 mappable reads, 429 mapped (429 unique mapping)
[M::scg_read_alignment] 65248 mappable reads, 429 mapped (429 unique mapping)
[M::syncasm] syncmer graph stats after final processing
[M::scg_stat] number unitigs  : 18
[M::scg_stat] number syncmers : 113
[M::scg_stat] number arcs     : 28
[M::annot_worker_pipeline] 18 sequences (86446 bp) loaded in 1 batch
[W::gfa_parse_L] the coverage of arc 'u7-' -> 'u7-' is zero
[W::gfa_parse_L] the coverage of arc 'u7+' -> 'u7+' is zero
[W::gfa_parse_L] the coverage of arc 'u13-' -> 'u13-' is zero
[W::gfa_parse_L] the coverage of arc 'u13+' -> 'u13+' is zero
[M::main] Version: 1.0
[M::main] CMD: oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam input_1//ch.fastq
[M::main] Real time: 58.334 sec; CPU: 18.447 sec; Peak RSS: 1.130 GB
+ '[' input_2/ont-ds-telo-contigs.bp.p_ctg.fa '!=' '' ']'
++ wc -l
++ grep '[.]gz$'
++ echo input_2/ont-ds-telo-contigs.bp.p_ctg.fa
++ true
+ '[' 0 = 1 ']'
+ sed 's/\r//'
+ awk '{if($0~"^>"){sub(/ .*/,"",$0)}; print $0}' input_2/ont-ds-telo-contigs.bp.p_ctg.fa
+ input_2=input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ cat oatk.asm.mito.ctg.fasta
+ sed 's/\t/ /g'
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ awk '-F\t' '{print ">mitochondrion_"$1"\n"$2}'
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_014842_370_15078
+ echo pp20250515_014842_370_15078
++ id -u
++ id -g
+ docker run --name pp20250515_014842_370_15078 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab
+ '[' -e oatk.asm.pltd.ctg.fasta ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -x asm10 plastid.fa input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa -t 8
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.28--h577a1d6_4
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_014843_231_29122
+ echo pp20250515_014843_231_29122
++ id -u
++ id -g
+ docker run --name pp20250515_014843_231_29122 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -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 -x asm10 plastid.fa input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa -t 8
[M::mm_idx_gen::0.001*62.89] collected minimizers
[M::mm_idx_gen::0.002*25.79] sorted minimizers
[M::main::0.002*25.70] loaded/built the index for 0 target sequence(s)
[M::mm_mapopt_update::0.002*25.51] mid_occ = 500
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 0
[M::mm_idx_stat::0.002*25.19] distinct minimizers: 0 (-nan% are singletons); average occurrences: -nan; average spacing: -nan; total length: 0
[M::worker_pipeline::1.552*4.18] mapped 370 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x asm10 -t 8 plastid.fa input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
[M::main] Real time: 1.554 sec; CPU: 6.488 sec; Peak RSS: 0.878 GB
+ cat plastid.fa.minimap2
+ awk '-F\t' '{len[$1]=$2; n[$1]++; hit1[$1][n[$1]]=$3; hit2[$1][n[$1]]=$4} END{for(i in n){PROCINFO["sorted_in"]="@val_num_asc"; oldstart=-1; oldend=-1; alignlen=0; for(j in hit1[i]){if(hit1[i][j]0.5){contami=1}else{contami=0}; print i"\t"len[i]"\t"alignlen"\t"percent"\t"contami}}'
+ sort -k1,1
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ awk '-F\t' 'FILENAME==ARGV[1]&&$5==1{contami[$1]=1} FILENAME==ARGV[2]&&contami[$1]!=1{print ">"$1"\n"$2}' plastid.fa.minimap2.contami /dev/stdin
++ date +%Y%m%d_%H%M%S_%3N
++ basename input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ PPDOCNAME=pp20250515_014845_387_27876
+ echo pp20250515_014845_387_27876
++ id -u
++ id -g
+ docker run --name pp20250515_014845_387_27876 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
++ basename input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ cat ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa.rem.fa plastid.fa
++ basename input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/assemble~oatk/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit



PID: 150147
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'assemble~oatk' -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa -p embryophyta_pltd.fam input_1/
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk
Containers: c2997108/oatk:1.0 centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ input_hifi=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' '' = '' ']'
+ input_hifi=input_1//ch.fastq
+ read i
+ echo HiFi reads: input_1//ch.fastq
HiFi reads: input_1//ch.fastq
+ optpltd=
+ '[' embryophyta_pltd.fam '!=' '' ']'
/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk: 行 41: p: 未割り当ての変数です

PID: 150566
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'assemble~oatk' -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa -p embryophyta_pltd.fam input_1/
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk
Containers: c2997108/oatk:1.0 centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ input_hifi=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' '' = '' ']'
+ input_hifi=input_1//ch.fastq
+ read i
+ echo HiFi reads: input_1//ch.fastq
HiFi reads: input_1//ch.fastq
+ optpltd=
+ '[' embryophyta_pltd.fam '!=' '' ']'
+ optpltd='-p /usr/local/oatkdb/embryophyta_pltd.fam'
+ FUNC_RUN_DOCKER c2997108/oatk:1.0 oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam -p /usr/local/oatkdb/embryophyta_pltd.fam input_1//ch.fastq
+ PP_RUN_IMAGE=c2997108/oatk:1.0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_015352_789_3244
+ echo pp20250515_015352_789_3244
++ id -u
++ id -g
+ docker run --name pp20250515_015352_789_3244 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/oatk:1.0 oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam -p /usr/local/oatkdb/embryophyta_pltd.fam input_1//ch.fastq
[M::syncasm] collected syncmers from 250000 target sequence(s)
[M::sr_db_stat] number syncmers collected: 2118029
[M::sr_db_stat] number syncmers per read: 8.472
[M::sr_db_stat] average kmer space: -631.569
[M::sr_db_stat] number uniqe smer: 422779; singletons: 247137 (58.455%)
[M::sr_db_stat] average smer count: 5.010
[M::sr_db_stat] smer peak_hom: 33; peak_het: 30
[M::sr_db_stat] number uniqe kmer: 1483824; singletons: 1329719 (89.614%)
[M::sr_db_stat] average kmer count: 1.427
[M::sr_db_stat] kmer peak_hom: 14; peak_het: -1
[M::find_error_syncmers] error syncmer candidates: num = 1483557, max_c = 109
[M::read_error_correction] Error Correction Summary Results
[M::read_error_correction] total number of error blocks : 17934
[M::read_error_correction]                - uncorrected : 4546
[M::read_error_correction]                  - corrected : 13228
[M::read_error_correction]             - ambiguous seqs : 2
[M::read_error_correction]             - ambiguous path : 1
[M::sr_db_stat] number syncmers collected: 2143337
[M::sr_db_stat] number syncmers per read: 8.573
[M::sr_db_stat] average kmer space: -632.918
[M::sr_db_stat] number uniqe smer: 421912; singletons: 246459 (58.415%)
[M::sr_db_stat] average smer count: 5.080
[M::sr_db_stat] smer peak_hom: 33; peak_het: 30
[M::sr_db_stat] number uniqe kmer: 1464186; singletons: 1310879 (89.530%)
[M::sr_db_stat] average kmer count: 1.464
[M::sr_db_stat] kmer peak_hom: 17; peak_het: 14
[M::syncasm] make syncmer graph
[M::syncasm] syncmer graph stats
[M::scg_stat] number unitigs  : 382
[M::scg_stat] number syncmers : 382
[M::scg_stat] number arcs     : 682
[M::syncasm] syncmer graph unitigging
[M::syncasm] syncmer graph stats after unitigging
[M::scg_stat] number unitigs  : 101
[M::scg_stat] number syncmers : 382
[M::scg_stat] number arcs     : 120
[M::syncasm] syncmer graph cleanup
[M::syncasm] assembly graph unzipping
[M::scg_read_alignment] 179303 mappable reads, 4729 mapped (4729 unique mapping)
[M::scg_read_alignment] 179303 mappable reads, 742 mapped (742 unique mapping)
[M::scg_read_alignment] 179303 mappable reads, 4729 mapped (4729 unique mapping)
[M::scg_read_alignment] 179303 mappable reads, 4729 mapped (4729 unique mapping)
[M::syncasm] syncmer graph stats after final processing
[M::scg_stat] number unitigs  : 48
[M::scg_stat] number syncmers : 243
[M::scg_stat] number arcs     : 102
[M::annot_worker_pipeline] 48 sequences (179328 bp) loaded in 2 batches
[M::annot_worker_pipeline] 48 sequences (179328 bp) loaded in 2 batches
[W::gfa_parse_L] the coverage of arc 'u10-' -> 'u10-' is zero
[W::gfa_parse_L] the coverage of arc 'u10+' -> 'u10+' is zero
[W::gfa_parse_L] the coverage of arc 'u11-' -> 'u11-' is zero
[W::gfa_parse_L] the coverage of arc 'u11+' -> 'u11+' is zero
[W::gfa_parse_L] the coverage of arc 'u12-' -> 'u12-' is zero
[W::gfa_parse_L] the coverage of arc 'u12+' -> 'u12+' is zero
[W::gfa_parse_L] the coverage of arc 'u14-' -> 'u14-' is zero
[W::gfa_parse_L] the coverage of arc 'u14+' -> 'u14+' is zero
[W::gfa_parse_L] the coverage of arc 'u22-' -> 'u22-' is zero
[W::gfa_parse_L] the coverage of arc 'u22+' -> 'u22+' is zero
[W::gfa_parse_L] the coverage of arc 'u24-' -> 'u24-' is zero
[W::gfa_parse_L] the coverage of arc 'u24+' -> 'u24+' is zero
[W::gfa_parse_L] the coverage of arc 'u25-' -> 'u25-' is zero
[W::gfa_parse_L] the coverage of arc 'u25+' -> 'u25+' is zero
[W::gfa_parse_L] the coverage of arc 'u26-' -> 'u26-' is zero
[W::gfa_parse_L] the coverage of arc 'u26+' -> 'u26+' is zero
[W::gfa_parse_L] the coverage of arc 'u27-' -> 'u27-' is zero
[W::gfa_parse_L] the coverage of arc 'u27+' -> 'u27+' is zero
[W::gfa_parse_L] the coverage of arc 'u29-' -> 'u29-' is zero
[W::gfa_parse_L] the coverage of arc 'u29+' -> 'u29+' is zero
[W::gfa_parse_L] the coverage of arc 'u30-' -> 'u30-' is zero
[W::gfa_parse_L] the coverage of arc 'u30+' -> 'u30+' is zero
[W::gfa_parse_L] the coverage of arc 'u31-' -> 'u31-' is zero
[W::gfa_parse_L] the coverage of arc 'u31+' -> 'u31+' is zero
[W::gfa_parse_L] the coverage of arc 'u36-' -> 'u36-' is zero
[W::gfa_parse_L] the coverage of arc 'u36+' -> 'u36+' is zero
[W::gfa_parse_L] the coverage of arc 'u44-' -> 'u45+' is zero
[W::gfa_parse_L] the coverage of arc 'u45-' -> 'u44+' is zero
[M::main] Version: 1.0
[M::main] CMD: oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam -p /usr/local/oatkdb/embryophyta_pltd.fam input_1//ch.fastq
[M::main] Real time: 169.628 sec; CPU: 63.910 sec; Peak RSS: 3.360 GB
+ '[' input_2/ont-ds-telo-contigs.bp.p_ctg.fa '!=' '' ']'
++ echo input_2/ont-ds-telo-contigs.bp.p_ctg.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ awk '{if($0~"^>"){sub(/ .*/,"",$0)}; print $0}' input_2/ont-ds-telo-contigs.bp.p_ctg.fa
+ sed 's/\r//'
+ input_2=input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ cat oatk.asm.mito.ctg.fasta
+ sed 's/\t/ /g'
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab
+ awk '-F\t' '{print ">mitochondrion_"$1"\n"$2}'
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_015644_373_20942
+ echo pp20250515_015644_373_20942
++ id -u
++ id -g
+ docker run --name pp20250515_015644_373_20942 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab
+ '[' -e oatk.asm.pltd.ctg.fasta ']'
+ cat oatk.asm.pltd.ctg.fasta
+ sed 's/\t/ /g'
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab
+ awk '-F\t' '{print ">chloroplast_"$1"\n"$2}'
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_015645_267_17336
+ echo pp20250515_015645_267_17336
++ id -u
++ id -g
+ docker run --name pp20250515_015645_267_17336 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -x asm10 plastid.fa input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa -t 8
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.28--h577a1d6_4
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_015645_962_16416
+ echo pp20250515_015645_962_16416
++ id -u
++ id -g
+ docker run --name pp20250515_015645_962_16416 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -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 -x asm10 plastid.fa input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa -t 8
[M::mm_idx_gen::0.008*8.52] collected minimizers
[M::mm_idx_gen::0.011*7.65] sorted minimizers
[M::main::0.011*7.64] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.012*6.98] mid_occ = 50
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.014*6.47] distinct minimizers: 10978 (93.10% are singletons); average occurrences: 1.069; average spacing: 10.020; total length: 117617
[M::worker_pipeline::1.632*4.74] mapped 370 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x asm10 -t 8 plastid.fa input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
[M::main] Real time: 1.637 sec; CPU: 7.741 sec; Peak RSS: 0.887 GB
+ cat plastid.fa.minimap2
+ awk '-F\t' '{len[$1]=$2; n[$1]++; hit1[$1][n[$1]]=$3; hit2[$1][n[$1]]=$4} END{for(i in n){PROCINFO["sorted_in"]="@val_num_asc"; oldstart=-1; oldend=-1; alignlen=0; for(j in hit1[i]){if(hit1[i][j]0.5){contami=1}else{contami=0}; print i"\t"len[i]"\t"alignlen"\t"percent"\t"contami}}'
+ sort -k1,1
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ awk '-F\t' 'FILENAME==ARGV[1]&&$5==1{contami[$1]=1} FILENAME==ARGV[2]&&contami[$1]!=1{print ">"$1"\n"$2}' plastid.fa.minimap2.contami /dev/stdin
++ date +%Y%m%d_%H%M%S_%3N
++ basename input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ PPDOCNAME=pp20250515_015648_224_1356
+ echo pp20250515_015648_224_1356
++ id -u
++ id -g
+ docker run --name pp20250515_015648_224_1356 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
++ basename input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ cat ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa.rem.fa plastid.fa
++ basename input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/assemble~oatk/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit

PID: 160142
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'assemble~oatk' -c 8 -m 32 -f input_2/ont-ds-telo-contigs.bp.p_ctg.fa -m embryophyta_mito.fam -p embryophyta_pltd.fam input_1/
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/assemble~oatk
Containers: c2997108/oatk:1.0 centos:centos6 quay.io/biocontainers/minimap2:2.28--h577a1d6_4 quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ input_hifi=
+ read i
++ find input_1//
++ egrep '[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' '' = '' ']'
+ input_hifi=input_1//ch.fastq
+ read i
+ echo HiFi reads: input_1//ch.fastq
HiFi reads: input_1//ch.fastq
+ optpltd=
+ '[' embryophyta_pltd.fam '!=' '' ']'
+ optpltd='-p /usr/local/oatkdb/embryophyta_pltd.fam'
+ FUNC_RUN_DOCKER c2997108/oatk:1.0 oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam -p /usr/local/oatkdb/embryophyta_pltd.fam input_1//ch.fastq
+ PP_RUN_IMAGE=c2997108/oatk:1.0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_020338_844_11001
+ echo pp20250515_020338_844_11001
++ id -u
++ id -g
+ docker run --name pp20250515_020338_844_11001 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/oatk:1.0 oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam -p /usr/local/oatkdb/embryophyta_pltd.fam input_1//ch.fastq
[M::syncasm] collected syncmers from 250000 target sequence(s)
[M::sr_db_stat] number syncmers collected: 2118029
[M::sr_db_stat] number syncmers per read: 8.472
[M::sr_db_stat] average kmer space: -631.569
[M::sr_db_stat] number uniqe smer: 422779; singletons: 247137 (58.455%)
[M::sr_db_stat] average smer count: 5.010
[M::sr_db_stat] smer peak_hom: 33; peak_het: 30
[M::sr_db_stat] number uniqe kmer: 1483824; singletons: 1329719 (89.614%)
[M::sr_db_stat] average kmer count: 1.427
[M::sr_db_stat] kmer peak_hom: 14; peak_het: -1
[M::find_error_syncmers] error syncmer candidates: num = 1483557, max_c = 109
[M::read_error_correction] Error Correction Summary Results
[M::read_error_correction] total number of error blocks : 17934
[M::read_error_correction]                - uncorrected : 4546
[M::read_error_correction]                  - corrected : 13228
[M::read_error_correction]             - ambiguous seqs : 2
[M::read_error_correction]             - ambiguous path : 1
[M::sr_db_stat] number syncmers collected: 2143337
[M::sr_db_stat] number syncmers per read: 8.573
[M::sr_db_stat] average kmer space: -632.918
[M::sr_db_stat] number uniqe smer: 421912; singletons: 246459 (58.415%)
[M::sr_db_stat] average smer count: 5.080
[M::sr_db_stat] smer peak_hom: 33; peak_het: 30
[M::sr_db_stat] number uniqe kmer: 1464186; singletons: 1310879 (89.530%)
[M::sr_db_stat] average kmer count: 1.464
[M::sr_db_stat] kmer peak_hom: 17; peak_het: 14
[M::syncasm] make syncmer graph
[M::syncasm] syncmer graph stats
[M::scg_stat] number unitigs  : 382
[M::scg_stat] number syncmers : 382
[M::scg_stat] number arcs     : 682
[M::syncasm] syncmer graph unitigging
[M::syncasm] syncmer graph stats after unitigging
[M::scg_stat] number unitigs  : 101
[M::scg_stat] number syncmers : 382
[M::scg_stat] number arcs     : 120
[M::syncasm] syncmer graph cleanup
[M::syncasm] assembly graph unzipping
[M::scg_read_alignment] 179303 mappable reads, 4729 mapped (4729 unique mapping)
[M::scg_read_alignment] 179303 mappable reads, 742 mapped (742 unique mapping)
[M::scg_read_alignment] 179303 mappable reads, 4729 mapped (4729 unique mapping)
[M::scg_read_alignment] 179303 mappable reads, 4729 mapped (4729 unique mapping)
[M::syncasm] syncmer graph stats after final processing
[M::scg_stat] number unitigs  : 48
[M::scg_stat] number syncmers : 243
[M::scg_stat] number arcs     : 102
[M::annot_worker_pipeline] 48 sequences (179328 bp) loaded in 2 batches
[M::annot_worker_pipeline] 48 sequences (179328 bp) loaded in 2 batches
[W::gfa_parse_L] the coverage of arc 'u10-' -> 'u10-' is zero
[W::gfa_parse_L] the coverage of arc 'u10+' -> 'u10+' is zero
[W::gfa_parse_L] the coverage of arc 'u11-' -> 'u11-' is zero
[W::gfa_parse_L] the coverage of arc 'u11+' -> 'u11+' is zero
[W::gfa_parse_L] the coverage of arc 'u12-' -> 'u12-' is zero
[W::gfa_parse_L] the coverage of arc 'u12+' -> 'u12+' is zero
[W::gfa_parse_L] the coverage of arc 'u14-' -> 'u14-' is zero
[W::gfa_parse_L] the coverage of arc 'u14+' -> 'u14+' is zero
[W::gfa_parse_L] the coverage of arc 'u22-' -> 'u22-' is zero
[W::gfa_parse_L] the coverage of arc 'u22+' -> 'u22+' is zero
[W::gfa_parse_L] the coverage of arc 'u24-' -> 'u24-' is zero
[W::gfa_parse_L] the coverage of arc 'u24+' -> 'u24+' is zero
[W::gfa_parse_L] the coverage of arc 'u25-' -> 'u25-' is zero
[W::gfa_parse_L] the coverage of arc 'u25+' -> 'u25+' is zero
[W::gfa_parse_L] the coverage of arc 'u26-' -> 'u26-' is zero
[W::gfa_parse_L] the coverage of arc 'u26+' -> 'u26+' is zero
[W::gfa_parse_L] the coverage of arc 'u27-' -> 'u27-' is zero
[W::gfa_parse_L] the coverage of arc 'u27+' -> 'u27+' is zero
[W::gfa_parse_L] the coverage of arc 'u29-' -> 'u29-' is zero
[W::gfa_parse_L] the coverage of arc 'u29+' -> 'u29+' is zero
[W::gfa_parse_L] the coverage of arc 'u30-' -> 'u30-' is zero
[W::gfa_parse_L] the coverage of arc 'u30+' -> 'u30+' is zero
[W::gfa_parse_L] the coverage of arc 'u31-' -> 'u31-' is zero
[W::gfa_parse_L] the coverage of arc 'u31+' -> 'u31+' is zero
[W::gfa_parse_L] the coverage of arc 'u36-' -> 'u36-' is zero
[W::gfa_parse_L] the coverage of arc 'u36+' -> 'u36+' is zero
[W::gfa_parse_L] the coverage of arc 'u44-' -> 'u45+' is zero
[W::gfa_parse_L] the coverage of arc 'u45-' -> 'u44+' is zero
[M::main] Version: 1.0
[M::main] CMD: oatk -o oatk.asm -t 8 -m /usr/local/oatkdb/dikarya_mito.fam -p /usr/local/oatkdb/embryophyta_pltd.fam input_1//ch.fastq
[M::main] Real time: 169.158 sec; CPU: 63.158 sec; Peak RSS: 3.342 GB
+ '[' input_2/ont-ds-telo-contigs.bp.p_ctg.fa '!=' '' ']'
++ echo input_2/ont-ds-telo-contigs.bp.p_ctg.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ awk '{if($0~"^>"){sub(/ .*/,"",$0)}; print $0}' input_2/ont-ds-telo-contigs.bp.p_ctg.fa
+ sed 's/\r//'
+ input_2=input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ cat oatk.asm.mito.ctg.fasta
+ sed 's/\t/ /g'
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab
+ awk '-F\t' '{print ">mitochondrion_"$1"\n"$2}'
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_020629_971_29321
+ echo pp20250515_020629_971_29321
++ id -u
++ id -g
+ docker run --name pp20250515_020629_971_29321 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab
+ '[' -e oatk.asm.pltd.ctg.fasta ']'
+ cat oatk.asm.pltd.ctg.fasta
+ sed 's/\t/ /g'
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab
+ awk '-F\t' '{print ">chloroplast_"$1"\n"$2}'
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_020630_838_18995
+ echo pp20250515_020630_838_18995
++ id -u
++ id -g
+ docker run --name pp20250515_020630_838_18995 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.28--h577a1d6_4 minimap2 -x asm10 plastid.fa input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa -t 8
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.28--h577a1d6_4
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250515_020631_492_14636
+ echo pp20250515_020631_492_14636
++ id -u
++ id -g
+ docker run --name pp20250515_020631_492_14636 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -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 -x asm10 plastid.fa input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa -t 8
[M::mm_idx_gen::0.013*5.20] collected minimizers
[M::mm_idx_gen::0.016*5.29] sorted minimizers
[M::main::0.016*5.28] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.018*4.92] mid_occ = 50
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.019*4.66] distinct minimizers: 10978 (93.10% are singletons); average occurrences: 1.069; average spacing: 10.020; total length: 117617
[M::worker_pipeline::1.591*4.84] mapped 370 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x asm10 -t 8 plastid.fa input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
[M::main] Real time: 1.594 sec; CPU: 7.706 sec; Peak RSS: 0.888 GB
+ cat plastid.fa.minimap2
+ sort -k1,1
+ awk '-F\t' '{len[$1]=$2; n[$1]++; hit1[$1][n[$1]]=$3; hit2[$1][n[$1]]=$4} END{for(i in n){PROCINFO["sorted_in"]="@val_num_asc"; oldstart=-1; oldend=-1; alignlen=0; for(j in hit1[i]){if(hit1[i][j]0.5){contami=1}else{contami=0}; print i"\t"len[i]"\t"alignlen"\t"percent"\t"contami}}'
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ awk '-F\t' 'FILENAME==ARGV[1]&&$5==1{contami[$1]=1} FILENAME==ARGV[2]&&contami[$1]!=1{print ">"$1"\n"$2}' plastid.fa.minimap2.contami /dev/stdin
++ date +%Y%m%d_%H%M%S_%3N
++ basename input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ PPDOCNAME=pp20250515_020633_790_22922
+ echo pp20250515_020633_790_22922
++ id -u
++ id -g
+ docker run --name pp20250515_020633_790_22922 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/assemble~oatk -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
++ basename input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ cat ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa.rem.fa plastid.fa
++ basename input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/assemble~oatk/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit