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No module named '_cffi_backend' when running somatic_variant_calling #477

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mbenary opened this issue Jan 8, 2024 · 1 comment
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@mbenary
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mbenary commented Jan 8, 2024

Describe the bug
When running a batch analysis for somatic variant calling, it fails with the following error message: ModuleNotFoundError: No module named '_cffi_backend'

To Reproduce
Steps to reproduce the behavior:

  1. Start a snappy-pipeline with a step for somatic_variant_calling
  2. Start a batch analysis using slurm.
  3. Go to slurm_log for the run-step.
  4. See error right after Activating environment

Expected behavior
The wrapper for somatic_variant_calling should be started and create a DAG of jobs for mutect2.

Additional context
This seems to be a combination of GATK (mutect2) and parallel jobs and / or snakemake. The step contamination in this workflow runs without error. This step also uses GATK but does not include parallelization.
The step mbcs which also relies on GATK has a dependency cffi in its wrapper, which might be necessary for the mutect2-wrapper.

ericblanc20 added a commit that referenced this issue Mar 20, 2024
Co-authored-by: Manuela Benary <manuela.benary@bihealth.de>
@ericblanc20
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Fixed (and all dependencies were reviewed in PR #492)

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