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difficulty while running docker image #1

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zyxNo1 opened this issue Jul 3, 2024 · 0 comments
Open

difficulty while running docker image #1

zyxNo1 opened this issue Jul 3, 2024 · 0 comments

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@zyxNo1
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zyxNo1 commented Jul 3, 2024

I download the docker image and tried to run germline pipeline of DIVIS following the guideline in README.
First, I tried the substeps in DIVIS. I tried to call variants by gatk after align step is done:
divis substep -s gatk4_haplotypecaller_germline -c config -o result/
However, there are error messages:

Traceback (most recent call last):
  File "/usr/local/bin/divis", line 9, in <module>
    load_entry_point('DIVIS==0.1', 'console_scripts', 'divis')()
  File "/usr/local/lib/python3.5/dist-packages/DIVIS-0.1-py3.5.egg/divis/cli.py", line 41, in main
    cli()
  File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 700, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 680, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 1027, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 873, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 508, in invoke
    return callback(*args, **kwargs)
  File "/usr/local/lib/python3.5/dist-packages/DIVIS-0.1-py3.5.egg/divis/cli.py", line 22, in substep
    sub_step_run(step, preview, config_file, out_dir)
  File "/usr/local/lib/python3.5/dist-packages/DIVIS-0.1-py3.5.egg/divis/substep.py", line 17, in sub_step_run
    default_macros_file = DEFAULT_SUBSTEP_MACROS_DICT[step_name]
KeyError: 'gatk4_haplotypecaller_germline'

Then I tried running the whole pipeline:
divis pipeline -f wes_germline -p -c config -o result/
Still got error message:
can't find pipeline: wes_germline

What should I do?

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