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