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bcbio / bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
MIT License
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test_cwl_docker_joint_calling_workflow fails due to TypeError #186

Open hackdna opened 4 years ago

hackdna commented 4 years ago

Command:

pytest tests/test_cwl.py::test_cwl_docker_joint_calling_workflow

Stderr log:

Traceback (most recent call last):
  File "/usr/local/bin/bcbio_nextgen.py", line 230, in <module>
    runfn.process(kwargs["args"])
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/distributed/runfn.py", line 58, in process
    out = fn(*fnargs)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/utils.py", line 55, in wrapper
    return f(*args, **kwargs)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/distributed/multitasks.py", line 391, in compare_to_rm
    return validate.compare_to_rm(*args)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/variation/validate.py", line 176, in compare_to_rm
    eval_files = _run_rtg_eval(vrn_file, rm_file, rm_interval_file, base_dir, toval_data, vmethod)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/variation/validate.py", line 260, in _run_rtg_eval
    vrn_file, rm_file, interval_bed = _prepare_inputs(vrn_file, rm_file, rm_interval_file, base_dir, data)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/variation/validate.py", line 250, in _prepare_inputs
    interval_bed = _get_merged_intervals(rm_interval_file, vrn_file, base_dir, data)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/variation/validate.py", line 347, in _get_merged_intervals
    a_intervals = get_analysis_intervals(data, vrn_file, base_dir)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/variation/validate.py", line 405, in get_analysis_intervals
    callable_bed = _callable_from_gvcf(data, vrn_file, base_dir)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/variation/validate.py", line 397, in _callable_from_gvcf
    do.run(cmd.format(**locals()), "Convert gVCF to BED file of callable regions")
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; gvcf_regions.py --gvcf_type gatk /cromwell-executions/main-gvcf-joint.cwl/04c20a20-7bd4-445a-b0c1-9c190f9727a7/call-variantcall/shard-0/wf-variantcall.cwl/3a8ede4e-e385-4a9c-97f3-c946469012ff/call-compare_to_rm/execution/validate/Test1/gatk-haplotype/Test1.vcf.gz | bedtools merge > /cromwell-executions/main-gvcf-joint.cwl/04c20a20-7bd4-445a-b0c1-9c190f9727a7/call-variantcall/shard-0/wf-variantcall.cwl/3a8ede4e-e385-4a9c-97f3-c946469012ff/call-compare_to_rm/execution/bcbiotx/tmp1n5_2wqg/Test1-gcvf-coverage.bed
Traceback (most recent call last):
  File "/usr/local/share/bcbio-nextgen/anaconda/bin/gvcf_regions.py", line 260, in <module>
    gvcf_regions(*all_par)
  File "/usr/local/share/bcbio-nextgen/anaconda/bin/gvcf_regions.py", line 126, in gvcf_regions
    if not is_header(line) and is_considered(line, ignore_phrases):
  File "/usr/local/share/bcbio-nextgen/anaconda/bin/gvcf_regions.py", line 8, in is_header
    return line.startswith('#')
TypeError: startswith first arg must be bytes or a tuple of bytes, not str
' returned non-zero exit status 1.