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Workflows reporting "Connect timed out"

birgerbirger Member, Broadie, CGA-mod ✭✭✭

As part of a benchmarking effort we are running the Best Practice QC workflow on 1000 BRCA pairs. For two of those pairs, the workflows failed to launch, with a report of "Connect timed out". The pairs in question are BRCA-E2-A15T-TP-NB and BRCA-PL-A8LZ-TP-NB. I re-launched the workflows on just these two pairs, and they appear to be running correctly now (workflows still underway, but some of the constituent tasks have completed successfully.

This is being done in a controlled access workspace: broad-firecloud-broade/BenchmarkWorkspace_template_CloneTestSharing2.

The submission id associated with the two failed runs is: 7afeacc4-d787-4ca6-8e32-7acab85c1d1f

There are no workflow IDs for the two pairs because apparently the workflow was never launched.

This is part of a Benchmarking effort that we have been going to Alex for support for. He has dbGaP access and has read privileges for the workspace.

Issue · Github
by Geraldine_VdAuwera

Issue Number
1599
State
closed
Last Updated
Milestone
Array
Closed By
vdauwera

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Thanks for the report. Since this seems to be a transient issue, there's nothing we can do at the moment, but we'll keep track of these. If the exact same problem happens again, please post a comment in this thread. If possible, please provide screenshots showing status, any error messages etc.

  • birgerbirger Member, Broadie, CGA-mod ✭✭✭

    You can learn more about this failure by looking at the cromwell logs.

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