mapping-nanopore~minimap2

Minimap mapping for single-end read.

input_1:FASTA/FASTQ

input_1/transcripts.fa

>FBtr0070000 type=mRNA; loc=X:join(19961689..19961845,19963955..19964071,19964782..19964944,19965006..19965126,19965197..19965511,19965577..19966071,19966183..19967012,19967081..19967223,19967284..19968479); ID=FBtr0070000; name=Nep3-RA; dbxref=FlyBase:FBtr0070000,FlyBase_Annotation_IDs:CG9565-RA,REFSEQ:NM_078693,REFSEQ:NM_078693; MD5=6c3abf7c6ba8b1392a073c85365b2e75; length=3537; parent=FBgn0031081; release=r6.49; species=Dmel; 
AGAAGTACCACCCCACCACACCACACCACTTCCAAACAGTCCGATTCAAAGTCATAATTTCATTTGCATTTGAATAAATG
CATCCCAGGCACACCACCCTCTCACCACTCACACATCTAAGCTGCTCCGATTTTATGGTCCTTGGTATAGAGAAATTATG
ACGCGCTACAAGCAGACCGAATTCACGGAGGACGACTCGAGTTCCATCGGCGGCATTCAATTGAACGAAGCGACCGGCCA
TACGGGCATGCAGATACGCTACCACACCGCCCGGGCTACATGGAATTGGCGCTCGAGAAACAAGACGGAGAAATGGCTGC
TCATCACGACTTTTGTGATGGCCATCACGATCTTTACGCTGCTCATCGTCCTTTTCACAGATGGAGGCAGCAGCGATGCG
ACCAAGCACGTCCTTCACGTCCAGCCGCACCAAAAAGATTGTCCTTCCGGCAATGAGCTTCCTTGCTTGAACAAGCACTG
CATCTTCGCCTCGAGCGAGATCCTTAAATCGATCGATGTGACCGTGGATCCGTGCGATGACTTCTATGGATATTCCTGCA
ATCAATGGATCAAGAACAACCCCATTCCCGAGGGGAAATCCACGTGGGGTACGTTCGGCAAGCTGGAGCAGATGAACCAG
TTGATAATACGTAACGTACTGGAGAAGCCGGCAAAAAGCTTTAAGTCGGACGCGGAGCGGAAGGCTAAGGTTTACTATGA

input_2:FASTA

input_2/dmel-all-chromosome-r6.49.fasta

>2L type=golden_path; loc=2L:1..23513712; ID=2L; dbxref=GB:AE014134,GB:AE014134,REFSEQ:NT_033779; MD5=b6a98b7c676bdaa11ec9521ed15aff2b; length=23513712; release=r6.49; species=Dmel;
CGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGGGAGAAATATG
ATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAATGGTGGCGGATGAACGAGAT
GATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGC
GAGAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCGCAAACCCAAAAAGACAATAC
ACGACAGAGAGAGAGAGCAGCGGAGATATTTAGATTGCCTATTAAATATGATCGCGTATGCGAGAGTAGTGCCAACATAT
TGTGCTCTCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAAACCCAAATCGACAATGCACGACAGAGGAAG
CAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGGGAGAAATATGATCGCGTATGCGAGAGTAGTGC
CAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAATGGTGGCGGATGAACGAGATGATAATATATTCAAGTTGCCGC
TAATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGT

Command

mapping-nanopore~minimap2 -c 8 -m 32 -f '-x splice:hq -u' -g y input_1/transcripts.10.fa input_2/ref.fasta

Output

output.gtf

X	output.genepred	exon	19961297	19961600	.	+	.	gene_id "FBtr0307555"; transcript_id "FBtr0307555"; exon_number "1"; exon_id "FBtr0307555.1";
X	output.genepred	CDS	19961297	19961600	.	+	0	gene_id "FBtr0307555"; transcript_id "FBtr0307555"; exon_number "1"; exon_id "FBtr0307555.1";
X	output.genepred	exon	19963955	19964071	.	+	.	gene_id "FBtr0307555"; transcript_id "FBtr0307555"; exon_number "2"; exon_id "FBtr0307555.2";
X	output.genepred	CDS	19963955	19964071	.	+	2	gene_id "FBtr0307555"; transcript_id "FBtr0307555"; exon_number "2"; exon_id "FBtr0307555.2";
X	output.genepred	exon	19964782	19964920	.	+	.	gene_id "FBtr0307555"; transcript_id "FBtr0307555"; exon_number "3"; exon_id "FBtr0307555.3";
X	output.genepred	CDS	19964782	19964920	.	+	2	gene_id "FBtr0307555"; transcript_id "FBtr0307555"; exon_number "3"; exon_id "FBtr0307555.3";
X	output.genepred	start_codon	19961297	19961299	.	+	0	gene_id "FBtr0307555"; transcript_id "FBtr0307555"; exon_number "1"; exon_id "FBtr0307555.1";
X	output.genepred	exon	19961689	19961845	.	+	.	gene_id "FBtr0070000"; transcript_id "FBtr0070000"; exon_number "1"; exon_id "FBtr0070000.1";
X	output.genepred	CDS	19961689	19961845	.	+	0	gene_id "FBtr0070000"; transcript_id "FBtr0070000"; exon_number "1"; exon_id "FBtr0070000.1";
X	output.genepred	exon	19963955	19964071	.	+	.	gene_id "FBtr0070000"; transcript_id "FBtr0070000"; exon_number "2"; exon_id "FBtr0070000.2";

view all outputs

Log

pp mapping-nanopore~minimap2 -c 8 -m 32 -f '-x splice:hq  -u' -g y input_1/transcripts.10.fa input_2/ref.fasta 
/yoshitake/PortablePipeline/PortablePipeline/scripts/common.sh: eval: 行 343: 一致する `}' を探索中に予期しないファイル終了 (EOF) です
/yoshitake/PortablePipeline/PortablePipeline/scripts/common.sh: eval: 行 344: 構文エラー: 予期しないファイル終了 (EOF) です
Checking the realpath of input files.
0 splice:hq
0 '-u'\'''
biocontainers/bedtools:v2.28.0_cv2 c2997108/centos7:1-kentUtils centos:centos6 quay.io/biocontainers/minimap2:2.24--h7132678_1 quay.io/biocontainers/samtools:1.9--h10a08f8_12
using docker
++ docker pull quay.io/biocontainers/minimap2:2.24--h7132678_1
2.24--h7132678_1: Pulling from biocontainers/minimap2
c1a16a04cedd: Already exists
4ca545ee6d5d: Already exists
3480a93e7c0a: Pulling fs layer
3480a93e7c0a: Download complete
3480a93e7c0a: Pull complete
Digest: sha256:1f23d5cfbefb25ef4f9a0ee5b4f78d3b6cb0b3c955028d80e1d8b00bc97e299a
Status: Downloaded newer image for quay.io/biocontainers/minimap2:2.24--h7132678_1
quay.io/biocontainers/minimap2:2.24--h7132678_1
++ set +ex
+ set -o pipefail
+ fq=splice:hq
+ ref='-u'\'''
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a '-u'\''' splice:hq
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.24--h7132678_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003451_641_30029
+ echo pp20230322_003451_641_30029
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ id -u
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003451_646_17657
+ echo pp20230322_003451_646_17657
++ id -u
++ id -g
++ id -g
+ docker run --name pp20230322_003451_646_17657 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ docker run --name pp20230322_003451_641_30029 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a '-u'\''' splice:hq
[ERROR][1;31m unrecognized cDNA direction[0m
++ onerror 30 -g y input_1/transcripts.10.fa input_2/ref.fasta
++ status=1
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-nanopore~minimap2
++ line=30
++ shift
++ set +x

------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-nanopore~minimap2 [Line 30]: Status 1

PID: 128478
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/mapping-nanopore~minimap2
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-nanopore~minimap2 "-g" "y" "input_1/transcripts.10.fa" "input_2/ref.fasta" 
------------------------------------------------------------

PID: 128472
pp runtime error.
/yoshitake/PortablePipeline/PortablePipeline/scripts/common.sh: eval: 行 343: 一致する `}' を探索中に予期しないファイル終了 (EOF) です
/yoshitake/PortablePipeline/PortablePipeline/scripts/common.sh: eval: 行 344: 構文エラー: 予期しないファイル終了 (EOF) です
Checking the realpath of input files.
0 input_1/transcripts.10.fa
0 input_2/ref.fasta
biocontainers/bedtools:v2.28.0_cv2 c2997108/centos7:1-kentUtils centos:centos6 quay.io/biocontainers/minimap2:2.24--h7132678_1 quay.io/biocontainers/samtools:1.9--h10a08f8_12
using docker
+ set -o pipefail
+ fq=input_1/transcripts.10.fa
+ ref=input_2/ref.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.24--h7132678_1
+ shift
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003547_564_31240
+ echo pp20230322_003547_564_31240
++ id -u
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003547_567_16956
+ echo pp20230322_003547_567_16956
++ id -u
++ id -g
++ id -g
+ docker run --name pp20230322_003547_567_16956 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
+ docker run --name pp20230322_003547_564_31240 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
[M::mm_idx_gen::0.812*1.03] collected minimizers
[M::mm_idx_gen::1.217*1.03] sorted minimizers
[M::main::1.217*1.03] loaded/built the index for 17 target sequence(s)
[M::mm_mapopt_update::1.285*1.03] mid_occ = 33
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 17
[M::mm_idx_stat::1.334*1.03] distinct minimizers: 2084917 (95.68% are singletons); average occurrences: 1.093; average spacing: 5.336; total length: 12157105
[M::worker_pipeline::1.384*1.00] mapped 10 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
[M::main] Real time: 1.405 sec; CPU: 1.408 sec; Peak RSS: 0.106 GB
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003550_470_19754
+ echo pp20230322_003550_470_19754
++ id -u
++ id -g
+ docker run --name pp20230322_003550_470_19754 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003552_025_8595
+ echo pp20230322_003552_025_8595
++ id -u
++ id -g
+ docker run --name pp20230322_003552_025_8595 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ '[' y = y ']'
+ FUNC_RUN_DOCKER biocontainers/bedtools:v2.28.0_cv2 bedtools bamtobed -bed12 -i output.bam
+ PP_RUN_IMAGE=biocontainers/bedtools:v2.28.0_cv2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003554_046_26083
+ echo pp20230322_003554_046_26083
++ id -u
++ id -g
+ docker run --name pp20230322_003554_046_26083 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm biocontainers/bedtools:v2.28.0_cv2 bedtools bamtobed -bed12 -i output.bam
+ FUNC_RUN_DOCKER c2997108/centos7:1-kentUtils bedToGenePred output.bed output.genepred
+ PP_RUN_IMAGE=c2997108/centos7:1-kentUtils
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003555_645_19755
+ echo pp20230322_003555_645_19755
++ id -u
++ id -g
+ docker run --name pp20230322_003555_645_19755 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm c2997108/centos7:1-kentUtils bedToGenePred output.bed output.genepred
+ FUNC_RUN_DOCKER c2997108/centos7:1-kentUtils genePredToGtf file output.genepred output.gtf
+ PP_RUN_IMAGE=c2997108/centos7:1-kentUtils
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003557_226_18585
+ echo pp20230322_003557_226_18585
++ id -u
++ id -g
+ docker run --name pp20230322_003557_226_18585 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm c2997108/centos7:1-kentUtils genePredToGtf file output.genepred output.gtf
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /yoshitake/test/mapping-nanopore~minimap2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 129121
/yoshitake/PortablePipeline/PortablePipeline/scripts/common.sh: eval: 行 343: 一致する `}' を探索中に予期しないファイル終了 (EOF) です
/yoshitake/PortablePipeline/PortablePipeline/scripts/common.sh: eval: 行 344: 構文エラー: 予期しないファイル終了 (EOF) です
Checking the realpath of input files.
0 input_1/transcripts.10.fa
0 input_2/ref.fasta
biocontainers/bedtools:v2.28.0_cv2 c2997108/centos7:1-kentUtils centos:centos6 quay.io/biocontainers/minimap2:2.24--h7132678_1 quay.io/biocontainers/samtools:1.9--h10a08f8_12
using docker
+ set -o pipefail
+ fq=input_1/transcripts.10.fa
+ ref=input_2/ref.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.24--h7132678_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003842_606_20958
+ echo pp20230322_003842_606_20958
++ id -u
+ PPDOCNAME=pp20230322_003842_608_18212
+ echo pp20230322_003842_608_18212
++ id -u
++ id -g
+ docker run --name pp20230322_003842_606_20958 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
++ id -g
+ docker run --name pp20230322_003842_608_18212 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
[M::mm_idx_gen::0.804*1.05] collected minimizers
[M::mm_idx_gen::1.333*0.97] sorted minimizers
[M::main::1.333*0.97] loaded/built the index for 17 target sequence(s)
[M::mm_mapopt_update::1.397*0.97] mid_occ = 33
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 17
[M::mm_idx_stat::1.435*0.98] distinct minimizers: 2084917 (95.68% are singletons); average occurrences: 1.093; average spacing: 5.336; total length: 12157105
[M::worker_pipeline::1.483*0.95] mapped 10 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
[M::main] Real time: 1.508 sec; CPU: 1.431 sec; Peak RSS: 0.106 GB
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003846_301_24724
+ echo pp20230322_003846_301_24724
++ id -u
++ id -g
+ docker run --name pp20230322_003846_301_24724 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003848_065_18647
+ echo pp20230322_003848_065_18647
++ id -u
++ id -g
+ docker run --name pp20230322_003848_065_18647 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ '[' y = y ']'
+ FUNC_RUN_DOCKER biocontainers/bedtools:v2.28.0_cv2 bedtools bamtobed -bed12 -i output.bam
+ PP_RUN_IMAGE=biocontainers/bedtools:v2.28.0_cv2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003849_635_8938
+ echo pp20230322_003849_635_8938
++ id -u
++ id -g
+ docker run --name pp20230322_003849_635_8938 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm biocontainers/bedtools:v2.28.0_cv2 bedtools bamtobed -bed12 -i output.bam
+ FUNC_RUN_DOCKER c2997108/centos7:1-kentUtils bedToGenePred output.bed output.genepred
+ PP_RUN_IMAGE=c2997108/centos7:1-kentUtils
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003851_158_25330
+ echo pp20230322_003851_158_25330
++ id -u
++ id -g
+ docker run --name pp20230322_003851_158_25330 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm c2997108/centos7:1-kentUtils bedToGenePred output.bed output.genepred
+ FUNC_RUN_DOCKER c2997108/centos7:1-kentUtils genePredToGtf file output.genepred output.gtf
+ PP_RUN_IMAGE=c2997108/centos7:1-kentUtils
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003852_568_14668
+ echo pp20230322_003852_568_14668
++ id -u
++ id -g
+ docker run --name pp20230322_003852_568_14668 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm c2997108/centos7:1-kentUtils genePredToGtf file output.genepred output.gtf
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /yoshitake/test/mapping-nanopore~minimap2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 130389
/yoshitake/PortablePipeline/PortablePipeline/scripts/common.sh: eval: 行 343: 一致する `}' を探索中に予期しないファイル終了 (EOF) です
/yoshitake/PortablePipeline/PortablePipeline/scripts/common.sh: eval: 行 344: 構文エラー: 予期しないファイル終了 (EOF) です
Checking the realpath of input files.
0 input_1/transcripts.10.fa
0 input_2/ref.fasta
biocontainers/bedtools:v2.28.0_cv2 c2997108/centos7:1-kentUtils centos:centos6 quay.io/biocontainers/minimap2:2.24--h7132678_1 quay.io/biocontainers/samtools:1.9--h10a08f8_12
using docker
+ set -o pipefail
+ fq=input_1/transcripts.10.fa
+ ref=input_2/ref.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.24--h7132678_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003902_247_177
+ echo pp20230322_003902_247_177
++ id -u
++ id -g
+ PPDOCNAME=pp20230322_003902_250_11822
+ echo pp20230322_003902_250_11822
++ id -u
++ id -g
+ docker run --name pp20230322_003902_250_11822 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
+ docker run --name pp20230322_003902_247_177 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
[M::mm_idx_gen::0.814*1.03] collected minimizers
[M::mm_idx_gen::1.209*1.05] sorted minimizers
[M::main::1.209*1.05] loaded/built the index for 17 target sequence(s)
[M::mm_mapopt_update::1.281*1.04] mid_occ = 33
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 17
[M::mm_idx_stat::1.330*1.04] distinct minimizers: 2084917 (95.68% are singletons); average occurrences: 1.093; average spacing: 5.336; total length: 12157105
[M::worker_pipeline::1.352*1.03] mapped 10 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
[M::main] Real time: 1.373 sec; CPU: 1.418 sec; Peak RSS: 0.106 GB
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003905_305_25100
+ echo pp20230322_003905_305_25100
++ id -u
++ id -g
+ docker run --name pp20230322_003905_305_25100 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003906_681_5375
+ echo pp20230322_003906_681_5375
++ id -u
++ id -g
+ docker run --name pp20230322_003906_681_5375 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ '[' n = y ']'
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /yoshitake/test/mapping-nanopore~minimap2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 131405
opt_c
opt_m
opt_f
/yoshitake/PortablePipeline/PortablePipeline/scripts/common.sh: eval: 行 344: 一致する `}' を探索中に予期しないファイル終了 (EOF) です
/yoshitake/PortablePipeline/PortablePipeline/scripts/common.sh: eval: 行 345: 構文エラー: 予期しないファイル終了 (EOF) です
opt_g
Checking the realpath of input files.
0 input_1/transcripts.10.fa
0 input_2/ref.fasta
biocontainers/bedtools:v2.28.0_cv2 c2997108/centos7:1-kentUtils centos:centos6 quay.io/biocontainers/minimap2:2.24--h7132678_1 quay.io/biocontainers/samtools:1.9--h10a08f8_12
using docker
+ set -o pipefail
+ fq=input_1/transcripts.10.fa
+ ref=input_2/ref.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.24--h7132678_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003941_087_8431
+ echo pp20230322_003941_087_8431
++ id -u
+ PPDOCNAME=pp20230322_003941_091_21368
+ echo pp20230322_003941_091_21368
++ id -u
++ id -g
++ id -g
+ docker run --name pp20230322_003941_091_21368 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ docker run --name pp20230322_003941_087_8431 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
[M::mm_idx_gen::0.815*1.03] collected minimizers
[M::mm_idx_gen::1.255*1.00] sorted minimizers
[M::main::1.255*1.00] loaded/built the index for 17 target sequence(s)
[M::mm_mapopt_update::1.325*1.00] mid_occ = 33
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 17
[M::mm_idx_stat::1.375*1.00] distinct minimizers: 2084917 (95.68% are singletons); average occurrences: 1.093; average spacing: 5.336; total length: 12157105
[M::worker_pipeline::1.406*0.99] mapped 10 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -t 8 -a input_2/ref.fasta input_1/transcripts.10.fa
[M::main] Real time: 1.428 sec; CPU: 1.408 sec; Peak RSS: 0.106 GB
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003944_138_10771
+ echo pp20230322_003944_138_10771
++ id -u
++ id -g
+ docker run --name pp20230322_003944_138_10771 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_003945_629_22384
+ echo pp20230322_003945_629_22384
++ id -u
++ id -g
+ docker run --name pp20230322_003945_629_22384 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ '[' n = y ']'
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /yoshitake/test/mapping-nanopore~minimap2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 132197
Checking the realpath of input files.
0 input_1/transcripts.10.fa
0 input_2/ref.fasta
biocontainers/bedtools:v2.28.0_cv2 c2997108/centos7:1-kentUtils centos:centos6 quay.io/biocontainers/minimap2:2.24--h7132678_1 quay.io/biocontainers/samtools:1.9--h10a08f8_12
using docker
+ set -o pipefail
+ fq=input_1/transcripts.10.fa
+ ref=input_2/ref.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a -x splice:hq -u input_2/ref.fasta input_1/transcripts.10.fa
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.24--h7132678_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004058_281_20897
+ echo pp20230322_004058_281_20897
++ date +%Y%m%d_%H%M%S_%3N
++ id -u
+ PPDOCNAME=pp20230322_004058_283_31315
+ echo pp20230322_004058_283_31315
++ id -u
++ id -g
+ docker run --name pp20230322_004058_281_20897 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
++ id -g
+ docker run --name pp20230322_004058_283_31315 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a -x splice:hq -u input_2/ref.fasta input_1/transcripts.10.fa
[ERROR][1;31m unrecognized cDNA direction[0m
++ onerror 30
++ status=1
++ script=/yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-nanopore~minimap2
++ line=30
++ shift
++ set +x

------------------------------------------------------------
Error occured on /yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-nanopore~minimap2 [Line 30]: Status 1

PID: 133038
User: yoshitake.kazutoshi
Current directory: /yoshitake/test/mapping-nanopore~minimap2
Command line: /yoshitake/PortablePipeline/PortablePipeline/scripts/mapping-nanopore~minimap2 
------------------------------------------------------------

PID: 133036
pp runtime error.
Checking the realpath of input files.
0 input_1/transcripts.10.fa
0 input_2/ref.fasta
biocontainers/bedtools:v2.28.0_cv2 c2997108/centos7:1-kentUtils centos:centos6 quay.io/biocontainers/minimap2:2.24--h7132678_1 quay.io/biocontainers/samtools:1.9--h10a08f8_12
using docker
+ set -o pipefail
+ fq=input_1/transcripts.10.fa
+ ref=input_2/ref.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a -x splice:hq -u f input_2/ref.fasta input_1/transcripts.10.fa
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.24--h7132678_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004127_454_9250
+ echo pp20230322_004127_454_9250
+ PPDOCNAME=pp20230322_004127_454_22899
+ echo pp20230322_004127_454_22899
++ id -u
++ id -u
++ id -g
+ docker run --name pp20230322_004127_454_22899 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a -x splice:hq -u f input_2/ref.fasta input_1/transcripts.10.fa
++ id -g
+ docker run --name pp20230322_004127_454_9250 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
[M::mm_idx_gen::0.904*1.04] collected minimizers
[M::mm_idx_gen::2.092*0.79] sorted minimizers
[M::main::2.092*0.79] loaded/built the index for 17 target sequence(s)
[M::mm_mapopt_update::2.207*0.80] mid_occ = 33
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 17
[M::mm_idx_stat::2.276*0.81] distinct minimizers: 3788481 (95.52% are singletons); average occurrences: 1.095; average spacing: 2.930; total length: 12157105
[M::worker_pipeline::2.290*0.81] mapped 10 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -t 8 -a -x splice:hq -u f input_2/ref.fasta input_1/transcripts.10.fa
[M::main] Real time: 2.313 sec; CPU: 1.868 sec; Peak RSS: 0.173 GB
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004131_743_31961
+ echo pp20230322_004131_743_31961
++ id -u
++ id -g
+ docker run --name pp20230322_004131_743_31961 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004133_186_16757
+ echo pp20230322_004133_186_16757
++ id -u
++ id -g
+ docker run --name pp20230322_004133_186_16757 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ '[' y = y ']'
+ FUNC_RUN_DOCKER biocontainers/bedtools:v2.28.0_cv2 bedtools bamtobed -bed12 -i output.bam
+ PP_RUN_IMAGE=biocontainers/bedtools:v2.28.0_cv2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004134_862_30260
+ echo pp20230322_004134_862_30260
++ id -u
++ id -g
+ docker run --name pp20230322_004134_862_30260 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm biocontainers/bedtools:v2.28.0_cv2 bedtools bamtobed -bed12 -i output.bam
+ FUNC_RUN_DOCKER c2997108/centos7:1-kentUtils bedToGenePred output.bed output.genepred
+ PP_RUN_IMAGE=c2997108/centos7:1-kentUtils
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004136_229_29943
+ echo pp20230322_004136_229_29943
++ id -u
++ id -g
+ docker run --name pp20230322_004136_229_29943 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm c2997108/centos7:1-kentUtils bedToGenePred output.bed output.genepred
+ FUNC_RUN_DOCKER c2997108/centos7:1-kentUtils genePredToGtf file output.genepred output.gtf
+ PP_RUN_IMAGE=c2997108/centos7:1-kentUtils
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004137_480_7950
+ echo pp20230322_004137_480_7950
++ id -u
++ id -g
+ docker run --name pp20230322_004137_480_7950 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm c2997108/centos7:1-kentUtils genePredToGtf file output.genepred output.gtf
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /yoshitake/test/mapping-nanopore~minimap2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 133547
Checking the realpath of input files.
0 input_1/transcripts.10.fa
0 input_2/ref.fasta
biocontainers/bedtools:v2.28.0_cv2 c2997108/centos7:1-kentUtils centos:centos6 quay.io/biocontainers/minimap2:2.24--h7132678_1 quay.io/biocontainers/samtools:1.9--h10a08f8_12
using docker
+ set -o pipefail
+ fq=input_1/transcripts.10.fa
+ ref=input_2/ref.fasta
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ FUNC_RUN_DOCKER quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a -x splice:hq -u f input_2/ref.fasta input_1/transcripts.10.fa
+ PP_RUN_IMAGE=quay.io/biocontainers/minimap2:2.24--h7132678_1
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004319_638_12717
+ echo pp20230322_004319_638_12717
+ PPDOCNAME=pp20230322_004319_641_25969
+ echo pp20230322_004319_641_25969
++ id -u
++ id -u
++ id -g
++ id -g
+ docker run --name pp20230322_004319_641_25969 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o output.bam
+ docker run --name pp20230322_004319_638_12717 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/minimap2:2.24--h7132678_1 minimap2 -t 8 -a -x splice:hq -u f input_2/ref.fasta input_1/transcripts.10.fa
[M::mm_idx_gen::0.932*1.04] collected minimizers
[M::mm_idx_gen::1.408*1.21] sorted minimizers
[M::main::1.408*1.21] loaded/built the index for 17 target sequence(s)
[M::mm_mapopt_update::1.515*1.19] mid_occ = 33
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 17
[M::mm_idx_stat::1.585*1.19] distinct minimizers: 3788481 (95.52% are singletons); average occurrences: 1.095; average spacing: 2.930; total length: 12157105
[M::worker_pipeline::1.641*1.20] mapped 10 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -t 8 -a -x splice:hq -u f input_2/ref.fasta input_1/transcripts.10.fa
[M::main] Real time: 1.663 sec; CPU: 1.999 sec; Peak RSS: 0.173 GB
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004323_177_6671
+ echo pp20230322_004323_177_6671
++ id -u
++ id -g
+ docker run --name pp20230322_004323_177_6671 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index output.bam
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.9--h10a08f8_12
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004324_649_29112
+ echo pp20230322_004324_649_29112
++ id -u
++ id -g
+ docker run --name pp20230322_004324_649_29112 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools faidx input_2/ref.fasta
+ '[' y = y ']'
+ FUNC_RUN_DOCKER biocontainers/bedtools:v2.28.0_cv2 bedtools bamtobed -bed12 -i output.bam
+ PP_RUN_IMAGE=biocontainers/bedtools:v2.28.0_cv2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004326_246_8764
+ echo pp20230322_004326_246_8764
++ id -u
++ id -g
+ docker run --name pp20230322_004326_246_8764 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm biocontainers/bedtools:v2.28.0_cv2 bedtools bamtobed -bed12 -i output.bam
+ FUNC_RUN_DOCKER c2997108/centos7:1-kentUtils bedToGenePred output.bed output.genepred
+ PP_RUN_IMAGE=c2997108/centos7:1-kentUtils
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004327_626_7312
+ echo pp20230322_004327_626_7312
++ id -u
++ id -g
+ docker run --name pp20230322_004327_626_7312 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm c2997108/centos7:1-kentUtils bedToGenePred output.bed output.genepred
+ FUNC_RUN_DOCKER c2997108/centos7:1-kentUtils genePredToGtf file output.genepred output.gtf
+ PP_RUN_IMAGE=c2997108/centos7:1-kentUtils
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230322_004329_232_15514
+ echo pp20230322_004329_232_15514
++ id -u
++ id -g
+ docker run --name pp20230322_004329_232_15514 -v /yoshitake/test/mapping-nanopore~minimap2:/yoshitake/test/mapping-nanopore~minimap2 -w /yoshitake/test/mapping-nanopore~minimap2 -u 2007:600 -i --rm c2997108/centos7:1-kentUtils genePredToGtf file output.genepred output.gtf
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /yoshitake/test/mapping-nanopore~minimap2/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 134803