processing-for-variant-discovery-gatk4 workflow: fails repeatedly at SamToFastqAndBwaMem step
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?
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.
Please provide us with
We’ll be happy to take a closer look as soon as we can!
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
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?
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