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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:
Start a snappy-pipeline with a step for somatic_variant_calling
Start a batch analysis using slurm.
Go to slurm_log for the run-step.
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.
The text was updated successfully, but these errors were encountered:
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:
somatic_variant_calling
slurm_log
for therun
-step.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 dependencycffi
in its wrapper, which might be necessary for the mutect2-wrapper.The text was updated successfully, but these errors were encountered: