I've been trying to run the recommended Mutect2-PON workflow on 10 WGS samples, and the job is failing ONLY on the last shard (shard-9) of every M2 call, for all 10 M2 calls spawned from Mutect2.
Screenshot of an example of the M2 job status:
The stderr logs tend to be rather uninformative (most of them suddenly truncate, although one which went to attempt-12 actually hit a delocalization error).
I shared the workspace with GROUP_FireCloud-Support@firecloud.org. The workspace I'm working in is called "pd-wgs-workspace", and can be found in the project "pd-wgs-project". The submission ID for this job is 4ba3b45d-d8d2-49a7-a7a6-c32079f09aea, and similar errors also occurred in earlier runs.
Help would be much appreciated! :) This has been tough to debug because of the relatively long run time for this tool.
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