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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/exec.sh: line 43: 12 Segmentation fault (core dumped) wget ftp://[email protected]/bundle/oncotator/oncotator_v1_ds_April052016.tar.gz'

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

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Best Answers

  • jeffmengjeffmeng Broad
    Accepted Answer

    Yes, the Mutect2 in FireCloud has the option of running Oncotator.
    I've found a post from Feb 15 that addresses the problem of Oncotator keeping variants that were filtered out.
    https://gatkforums.broadinstitute.org/gatk/discussion/11440/m2-gatk4-oncotated-maf-output-includes-rejected-mutations/p1

Answers

  • 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?

  • jeffmengjeffmeng BroadMember, Broadie
    Accepted Answer

    Yes, the Mutect2 in FireCloud has the option of running Oncotator.
    I've found a post from Feb 15 that addresses the problem of Oncotator keeping variants that were filtered out.
    https://gatkforums.broadinstitute.org/gatk/discussion/11440/m2-gatk4-oncotated-maf-output-includes-rejected-mutations/p1

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