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Mutect2 Oncotator failed to delocalize files

jeffmengjeffmeng BroadMember, Broadie

I tried to run Mutect2 with Oncotator in FireCloud and it seems like Cromwell is having trouble copying files, though I don't know what that means. I got the following error message.

Task Mutect2.oncotate_m2:NA:1 failed. Job exit code 1. Check gs://fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a/e343f02f-89f4-42e4-8041-d92d91be3077/Mutect2/69442194-e6a1-4922-9419-7de4905bbce6/call-oncotate_m2/oncotate_m2-stderr.log for more information. PAPI error code 5. Message: 10: Failed to delocalize files: failed to copy the following files: "/mnt/local-disk/A1_t.maf.annotated -> gs://fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a/e343f02f-89f4-42e4-8041-d92d91be3077/Mutect2/69442194-e6a1-4922-9419-7de4905bbce6/call-oncotate_m2/A1_t.maf.annotated (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/A1_t.maf.annotated gs://fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a/e343f02f-89f4-42e4-8041-d92d91be3077/Mutect2/69442194-e6a1-4922-9419-7de4905bbce6/call-oncotate_m2/A1_t.maf.annotated, command failed: CommandException: No URLs matched: /mnt/local-disk/A1_t.maf.annotated\nCommandException: 1 file/object could not be transferred.\n)"``

I looked at the "oncotate_m2-stderr.log" and it ended with:

/cromwell_root/ line 43: 12 Segmentation fault (core dumped) wget'

Any idea what's going on and how I can fix it? Thanks!

This question is also posted on the GATK4 help forum here



  • jeffmengjeffmeng BroadMember, Broadie

    Update: Mutect2 successfully ran Oncotator after I followed a colleague's suggestion of setting the Mutect2 method configuration field “onco_ds_tar_gz” to "gs://gatk-best-practices/somatic-b37/oncotator_v1_ds_April052016.tar.gz". However, the MAF contained both filtered (by Mutect2) and unfiltered variants and did not distinguish them. Is there a fix to the problem?

  • KateNKateN Cambridge, MAMember, Broadie, Moderator

    Apologies for the delay-- I was typing up an answer to your original question when you updated with more information.

    The original error message PAPI error code 5. Message: 10: Failed to delocalize files indicates simply that something went wrong with your run. It asked you to check the oncotate_m2-stderr.log for more information. Unfortunately the last line you posted does not give me enough information to troubleshoot exactly what went wrong. I'd be happy to take a look if you could upload that error log.

    I'm assuming that your colleague's suggestion is the solution to the error you originally encountered, since your workflow successfully ran. (If you're not sure, though, feel free to share that original error log.) However, I'm not familiar with the logic of the workflow itself in order to give you an explanation of why filtered and unfiltered variants were output together. I will ask a colleague of mine to take a look.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator

    My colleague has told me that Mutect2 no longer produces a MAF file as of the GATK4 official release. Unfortunately, I cannot assist with diagnosing old Mutect2 workflows not published by us, but I can recommend using our currently featured Mutect2 workflow. You can find a workspace with it all set up here.

  • jeffmengjeffmeng BroadMember, Broadie

    @KateN Thanks for your reply. I am actually using the Mutect2 in GATK4, the same as the one in your workspace. The Mutect2 method has the option of running Oncotator, which takes the Mutect2 VCF to make a MAF. Mutect2 produces both a filtered and unfiltered VCF. It seems that the filtering information is lost in the MAF.

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