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subprocess.CalledProcessError: Command '['bcftools', 'index', '/mnt/variantgrid/data/import_processing/pipeline_7783/split_vcf/dragen_mutect_vardict_shared00.vcf.gz']' returned non-zero exit status 255. #1190

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davmlaw opened this issue Nov 6, 2024 · 0 comments

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@davmlaw
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davmlaw commented Nov 6, 2024

View details in Rollbar: https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/5480

UploadPipeline 7783 failed. Filename: VCF Error: Error executing: Command '['bcftools', 'index', '/mnt/variantgrid/data/import_processing/pipeline_7783/split_vcf/dragen_mutect_vardict_shared00.vcf.gz']' returned non-zero exit status 255.
Traceback (most recent call last):
  File "/mnt/variantgrid/upload/tasks/vcf/import_vcf_step_task.py", line 73, in run
    items_processed = self.process_items(upload_step)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/variantgrid/upload/tasks/vcf/unknown_variants_task.py", line 115, in process_items
    subprocess.run(cmd_index, capture_output=True, check=True)
  File "/usr/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['bcftools', 'index', '/mnt/variantgrid/data/import_processing/pipeline_7783/split_vcf/dragen_mutect_vardict_shared00.vcf.gz']' returned non-zero exit status 255.

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