A JAVA Error when running GATKSVPipelineBatch.wdl with GATKSVPipelineBatch.ref_panel_1kg.json

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2tong

• July 01, 2020 04:39

Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.

To whom it may concern:

When I try to test the GATKSVPipelineBatch.wdl with GATKSVPipelineBatch.ref_panel_1kg.json without melt, I got an error message:

Should I rewrite the wdl to solve this problem? If you have a good idea to solve this problem, please tell me.

Thank you very much.

ref: https://github.com/broadinstitute/gatk-sv/

 

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• 

  Jason Cerrato

  • July 02, 2020 13:32

  Hi 2tong,

  Happy to see if we can help here. Can you provide a few more details for us so we can better assist you?

  • Are you running this on a personal Cromwell?
  • Which version of GATK are you using?
  • You mentioned you aren't using melt. Are you using cromshell and womtool?
  • Have you disabled melt per the instructions in the documentation? https://github.com/broadinstitute/gatk-sv/#melt

  Many thanks,

  Jason

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