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broadinstitute / warp

WDL Analysis Research Pipelines
https://broadinstitute.github.io/warp
BSD 3-Clause "New" or "Revised" License
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return code 247 #1278

Open vzupan3 opened 4 months ago

vzupan3 commented 4 months ago

Hi! When running ExomeGermlineSingleSample_v3.1.19 on local machine I get an error: Job VariantCalling.HaplotypeCallerGATK4:2:1 exited with return code 247 which has not been declared as a valid return code. I tried to bring down # of scatters and try to modify CreateSequenceGroupingTSV task line 49 from "\n" to "\t" leading to a single row/group, leading to single shard/scatter, but that did not resolve the problem.

stderr.zip.

ekiernan commented 3 months ago

Hi, thanks for reaching out. We don't typically run locally, so we may not have as much feedback here as we would like, but we can certainly try. Could you please give us more information about your local machine:

  1. Hardware
  2. Memory
  3. CPU
  4. Disk

Could you also paste the error instead of posting the zip?

We also found this from stackovervlow: https://stackoverflow.com/questions/66785929/docker-container-exited-with-code-247-when-getting-data-from-gcp

We think you're on to something with scattering being a problem since you're on a local machine, but if your machine is running like a server, then that might not be a problem.

Thank you so much!