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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://gsapubftp-anonymous@ftp.broadinstitute.org/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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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?

  • shleeshlee CambridgeMember, Broadie, Moderator

    Just to be clear @jeffmeng, Mutect2 and Oncotator are separate tools. I presume you are referring to Mutect2 in relation to some script that includes an Oncotator task.

    GATK4 Mutect2 itself produces a VCF format callset, and it is incapable of producing a MAF.
    Within the VCF, calls that PASS, as well as those that are filtered after filtering by FilterMutectCalls, remain in the callset. Filtering tools write the reason for filtering in the FILTER column. This is to enable manual review, as is typical in somatic analyses. Default parameters of the workflow intentionally emit some calls that will be obviously filtered (negative training data) and filtering itself is intentionally stringent.

    Tutorial#11136 goes through such considerations.

  • jeffmengjeffmeng BroadMember, Broadie

    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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