leepc12
commented
2 years ago It looks like your genome TSV or TSS is not in a valid format. Use TAB instead of SPACE in the TSS file.
Example.
$ zcat /mnt/data/pipeline_genome_data/hg38/ataqc/hg38_gencode_v29_tss_unique.bed.gz | head
chr1 65417 65418 ENSG00000186092.6 0 +
chr1 451697 451698 ENSG00000284733.1 0 -
chr1 686673 686674 ENSG00000284662.1 0 -
chr1 923926 923927 ENSG00000187634.11 0 +
chr1 959309 959310 ENSG00000188976.10 0 -
chr1 960585 960586 ENSG00000187961.13 0 +
chr1 966495 966496 ENSG00000187583.10 0 +
chr1 982093 982094 ENSG00000187642.9 0 -
chr1 1000172 1000173 ENSG00000188290.10 0 -
chr1 1001136 1001137 ENSG00000187608.9 0 +
Describe the bug
when i append the tss file ,it show this mistake
OS/Platform
Caper configuration file
2022-04-11 21:37:00,784|caper.cli|INFO| Cromwell stdout: /home/zjin/atac/cromwell.out.2 2022-04-11 21:37:00,786|caper.caper_base|INFO| Creating a timestamped temporary directory. /home/zjin/atac/total-2/.caper_tmp/atac/20220411_213700_785801 2022-04-11 21:37:00,786|caper.caper_runner|INFO| Localizing files on work_dir. /home/zjin/atac/total-2/.caper_tmp/atac/20220411_213700_785801 2022-04-11 21:37:01,777|caper.caper_workflow_opts|INFO| Conda environment name found in WDL metadata. wdl=/home/zjin/atac/atac.wdl, s=encode-atac-seq-pipeline 2022-04-11 21:37:01,780|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool... 2022-04-11 21:37:05,192|caper.cromwell|INFO| Passed Womtool validation. 2022-04-11 21:37:05,194|caper.caper_runner|INFO| launching run: wdl=/home/zjin/atac/atac.wdl, inputs=/home/zjin/atac/atac.json, backend_conf=/home/zjin/atac/total-2/.caper_tmp/atac/20220411_213700_785801/backend.conf 2022-04-11 21:37:18,138|caper.cromwell_workflow_monitor|INFO| Workflow: id=4b3b3cdf-8c42-415b-9790-1621d79c1fe5, status=Submitted 2022-04-11 21:37:18,248|caper.cromwell_workflow_monitor|INFO| Workflow: id=4b3b3cdf-8c42-415b-9790-1621d79c1fe5, status=Running 2022-04-11 21:37:33,006|caper.cromwell_workflow_monitor|INFO| Task: id=4b3b3cdf-8c42-415b-9790-1621d79c1fe5, task=atac.read_genome_tsv:-1, retry=0, status=Started, job_id=57986 2022-04-11 21:37:33,013|caper.cromwell_workflow_monitor|INFO| Task: id=4b3b3cdf-8c42-415b-9790-1621d79c1fe5, task=atac.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode 2022-04-11 21:37:37,814|caper.cromwell_workflow_monitor|INFO| Task: id=4b3b3cdf-8c42-415b-9790-1621d79c1fe5, task=atac.read_genome_tsv:-1, retry=0, status=Done 2022-04-11 21:37:38,764|caper.cromwell_workflow_monitor|INFO| Workflow: id=4b3b3cdf-8c42-415b-9790-1621d79c1fe5, status=Failed 2022-04-11 21:37:54,026|caper.cromwell_metadata|INFO| Wrote metadata file. /home/zjin/atac/total-2/atac/4b3b3cdf-8c42-415b-9790-1621d79c1fe5/metadata.json 2022-04-11 21:37:54,027|caper.cromwell|INFO| Workflow failed. Auto-troubleshooting...
==== NAME=atac.read_genome_tsv, STATUS=Failed, PARENT= SHARD_IDX=-1, RC=1, JOB_ID=57986 START=2022-04-11T13:37:30.035Z, END=2022-04-11T13:37:37.844Z STDOUT=/home/zjin/atac/total-2/atac/4b3b3cdf-8c42-415b-9790-1621d79c1fe5/call-read_genome_tsv/execution/stdout STDERR=/home/zjin/atac/total-2/atac/4b3b3cdf-8c42-415b-9790-1621d79c1fe5/call-read_genome_tsv/execution/stderr STDERR_CONTENTS= Traceback (most recent call last): File "", line 6, in
ValueError: not enough values to unpack (expected 2, got 1)
STDERR_BACKGROUND_CONTENTS= Traceback (most recent call last): File "", line 6, in
ValueError: not enough values to unpack (expected 2, got 1)
2022-04-11 21:37:54,028|caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1 2022-04-11 21:37:54,029|caper.cli|ERROR| Check stdout in /home/zjin/atac/cromwell.out.2
Input JSON file
{
"atac.pipeline_type" : "atac", "atac.genome_tsv" : "/home/zjin/atac/yxiang_test/02.ensembl_susScr11_encode_atac_seq_no_scaffold/ensembl_susScr11_encode_atac_seq_no_scaffold.tsv", "atac.fastqs_rep1_R1" : ["/home/zjin/data/4-1/JM_R1.fq.gz"], "atac.fastqs_rep1_R2" : ["/home/zjin/data/4-1/JM_R2.fq.gz"], "atac.paired_end" : true, "atac.auto_detect_adapter" : true, "atac.enable_xcor" : true, "atac.title" : "test", "atac.description" :"wrsm ", "atac.gensz" : "2497530654"
}
tss.file
1 88626695 88650761 ENSECAG00000040809.1 0 + 1 89195185 89196911 ENSECAG00000033865.2 0 - 1 126616963 126728581 ENSECAG00000020259.3 0 - 1 89238505 89269098 ENSECAG00000034397.1 0 - 1 6434 15716 ENSECAG00000012421.3 0 + 1 158974107 159019894 ENSECAG00000042840.1 0 - 1 127055125 127057675 ENSECAG00000043695.1 0 - 1 159041627 159044523 ENSECAG00000030042.2 0 + 1 159049816 159051842 ENSECAG00000001454.2 0 + 1 159101630 159107451 ENSECAG00000001538.3 0 -
tsv.file
genome_name ensembl_susScr11_encode_atac_seq_no_scaffold ref_fa /home/zjin/atac/yxiang_test/02.ensembl_susScr11_encode_atac_seq_no_scaffold/./Equus_caballus.EquCab2.dna.toplevel.fa.gz ref_mito_fa /home/zjin/atac/yxiang_test/02.ensembl_susScr11_encode_atac_seq_no_scaffold/./Equus_caballus.EquCab2.dna.toplevel.MT.fa.gz mito_chr_name MT regex_bfilt_peak_chr_name .* chrsz /home/zjin/atac/yxiang_test/02.ensembl_susScr11_encode_atac_seq_no_scaffold/./ensembl_susScr11_encode_atac_seq_no_scaffold.chrom.sizes gensz 2474929062 bowtie2_idx_tar /home/zjin/atac/yxiang_test/02.ensembl_susScr11_encode_atac_seq_no_scaffold/./bowtie2_index/Equus_caballus.EquCab2.dna.toplevel.fa.tar.gz bowtie2_mito_idx_tar /home/zjin/atac/yxiang_test/02.ensembl_susScr11_encode_atac_seq_no_scaffold/./bowtie2_index/Equus_caballus.EquCab2.dna.toplevel.MT.fa.tar.gz tss /home/zjin/data/refsq/1.bed