processing-for-variant-discovery-gatk4 workflow: fails repeatedly at SamToFastqAndBwaMem step

Post author
Arun Seetharam

Hello,

I'm not sure if I'm doing something wrong, but I've been trying to test the GATK Best Practices Germline SNPs and INDELS with non-downsampled files, and it seems to have a problem at the BWA-mem mapping step. The mapping runs for 12-20hrs but then fails unexpectedly (see screenshot below). This happened 4 times so far and at this point, I've started doubting myself that I'm doing something really wrong. Could you please help?

Comments

4 comments

  • Comment author
    Samantha (she/her)

    Hi Arun Seetharam

    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,

    Samantha

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  • Comment author
    Arun Seetharam

    This was from another account. I've shared the workspace with the support, here are the details:

    1. Link to the workspace: https://app.terra.bio/#workspaces/GATK_test_run_2022-07-01/GATK4-B73v5-testing-20220704

    2. Submission-ID: 830d5d15-335a-4462-b71e-2c297c504be4

    3 Workflow ID: f2268f09-3570-4b70-84eb-0ccb680cc892

    Thank you!

    0
  • Comment author
    Samantha (she/her)

    Hi Arun Seetharam,

    It looks like the workspace is protected by an authorization domain named arun-gatk-testing. Can you please add Terra-Support@firecloud.org to that group so we can access the workspace?

    Thanks,
    Samantha

    0
  • Comment author
    Arun Seetharam

    Done!

    0

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