Hang occurs on WholeGenomeGermlineSingleSample

[innerpyg]

Hi

I am running WholeGenomeGermlineSingleSample.wdl via slurm hpc using cromwell_52.jar and i am currently facing two issues.

1. It seems that after GatherBam of UnmappedBamToAlignedBam, it does not run the sub-workflow BamToCram.
2. According to the log, after variantcall final output checking, it does not go to the next step and hangs.

I think the workflow will not complete because of #1.
Do you have any idea?

I share the log file below.
WholeGenomeGermlineSingleSample.log

Thanks

[innerpyg]

Hi,

The problem has been solved.

I don't know the exact cause, but I changed it to cromwell-86.jar and rewrote the json file and it worked fine.

Thanks

[jessicaway]

Thanks for updating with the fix! Closing for now, but please reopen if you see the issues continue