gatk4-rnaseq-germline-snps-indels gtfToCallingIntervals memory error

Post author
Jaclyn Long

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! 

Comments

4 comments

  • Comment author
    Pamela Bretscher

    Hi Jaclyn,

    Thanks for writing in with this issue! A member of the Terra support team will follow up with you as soon as they are able.

    If relevant, please let us know if there is any urgency around this request so that the team can prioritize it appropriately.

    Kind regards,

    Pamela

    0
  • Comment author
    Shoaib Rakhangi

    Hi Jaclyn,

     

    Thank you for writing in about this issue. Can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

    1. Toggle the "Share with support" button to "Yes"
    2. Click Save

     

    Please provide us with

    1. A link to your workspace
    2. The relevant submission ID
    3. The relevant workflow ID

     

    We’ll be happy to take a closer look as soon as we can!

     

    Kind regards,

    Shoaib

    0
  • Comment author
    Jaclyn Long

    Hello, 

    Thanks in advance for your help! I have shared the workspace with the support team. 

    Link: https://app.terra.bio/#workspaces/bch-rc-billing/Pediatric_COVID19 

    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

    0
  • Comment author
    Shoaib Rakhangi

    Hi Jaclyn,

    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?

    Kind regards,
    Shoaib

    0

Please sign in to leave a comment.