PAPI error code 2
Hello,
I am running into this recurring error while running the GATK CNV PoN workflow:
I attached the error message below-
This is happening after increasing the disk space and the preemptibles.
Happy to get any suggestions and see if others are encountering the same issue.
Thank you,
Yifat
Comments
6 comments
This is also the Failure message we see:
Hi Yifat and Luda,
Thank you for writing in about these. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace (see the icon with the three dots at the top-right)?
1. Add GROUP_FireCloud-Support@firecloud.org to the User email field and press enter on your keyboard
2. Click Save
Let us know the workspace name, as well as the relevant submission and workflow IDs. We'll be happy to take a look and get back to you as soon as we can.
Kind regards,
Jason
Hello Jason,
Thanks for responding.
We cannot share the workspace as this workspace contains restricted data.
Do you have any suggestions as to the error source?
Best,
Yifat
Hi Yifat,
Can you share the workflow ID(s) where you're receiving the error? We should be able to examine the error on the backend. It looks like there's a space issue specific to the docker.
Is the workflow you're using the very same from either Somatic-CNVs-GATK or Germline-CNVs-GATK, without modification?
Kind regards,
Jason
It seems for now that increasing the boot disk space is solving this error.
and yes we are using the GATK4 somatic CNVs workflow.
Thanks,
Yifat
Hi Yifat,
Thanks for letting us know. The boot disk not being big enough sounds about right for this issue since it was related to the docker. I'm glad you were able to figure it out!
If there's anything else that's unclear, please let me know.
Kind regards,
Jason
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