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FireCloud jobs fail with no stdout, stderr, and minimal JES log

ericco92ericco92 Cambridge, UKMember ✭✭

I'm seeing behavior similar to two previous posts:
https://gatkforums.broadinstitute.org/firecloud/discussion/10262/failure-to-delocalize-files-when-using-my-own-docker-image
https://gatkforums.broadinstitute.org/firecloud/discussion/8863/firecloud-ui-error-messages

In short, I have a tool that runs fine locally on a small example but dies silently in FireCloud on a larger one. I'm using ridiculously large local-disk and boot disk but it seems my tool is never running, as I expect to get stdout and stderr output (and see it locally).

One of my wdls / configurations is here: https://portal.firecloud.org/#methods/m/erictdawson/lumpyexpress-bamba-somatic/11

I can't share a full test dataset but I'm happy to help however else I can.

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