gatk4-rnaseq-germline-snps-indels gtfToCallingIntervals memory error
I am trying to run the gatk4-rnaseq-germline-snps-indels workflow to convert uBam files to VCF files. The gtfToCallingIntervals task keeps failing.
Within the Job Manager, I get the following Failure Message: stderr for job `RNAseq.gtfToCallingIntervals:NA:1` contained one of the `memory-retry-error-keys: [OutOfMemory,Killed]` specified in the Cromwell config. Job might have run out of memory.
The log file for the call-gtfToCallingIntervals is below.
I have tried increasing the star_mem_max_gb up to 500GB and the additional_disk to 100 GB. I am not sure if there are other memory parameters I should increase, or how to get closer to the root of the issue.
Any advice would be greatly appreciated!
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Thanks in advance for your help! I have shared the workspace with the support team.
I have tried this multiple times with different parameters, but here is an example submission:
Submission ID: 9c3f705c-145c-4b3c-845e-28f50cb01770
Workflow ID: ba771174-a600-4dd3-952a-872ab4fc558d
Sorry for the long wait. Do you have any other failing submission IDs you could provide, such as when you had a lower disk size?
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