/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]]=$4} END{for(i in n){PROCINFO["sorted_in"]="@val_num_asc"; oldstart=-1; oldend=-1; alignlen=0; for(j in hit1[i]){if(hit1[i][j]<oldend){oldend=hit2[i][j]}else{alignlen+=oldend-oldstart; oldstart=hit1[i][j]; oldend=hit2[i][j]}}; alignlen+=oldend-oldstart; percent=alignlen/len[i]; if(percent>0.5){contami=1}else{contami=0}; print i"\t"len[i]"\t"alignlen"\t"percent"\t"contami}}'
+ FUNC_RUN_DOCKER quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0 seqkit fx2tab input_2/ont-ds-telo-contigs.bp.p_ctg.fa.ref.fa
+ PP_RUN_IMAGE=quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ 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