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[GATK4] Mutect2 unable to evaluate gnomad_vcf_size

Hello,

I'm currently trying to run the "mutect2-gatk4" public method (snapshot ID 12), and I'm hitting the following error:

message: Failed to evaluate 'Mutect2.gnomad_vcf_size' (reason 1 of 1): Evaluating if defined(gnomad) then ceil(size(gnomad, "GB")) else 0 failed: gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz‎

even though that file exists.

I found a similar thread with an identical error message here, but the accepted answer doesn't apply to me; gatk_docker is mapped to my corresponding workspace attribute, which is the correctly versioned "us.gcr.io/broad-gatk/gatk:4.0.4.0".

Any ideas on why this error may be occurring?

Thank you!
Lee

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  • bshifawbshifaw moonMember, Broadie, Moderator admin

    Also see the following comment

  • lraolrao Member
    How did you setup the muctect2 method? Was the workspace cloned or was the method imported into a workspace you created? It may be related to a simple error when entering the file path for the method configuration. If the method was imported into a workspace be sure double quotes are being used.
    

    I imported the method into my workspace, and then filled in the method configuration by hand. I don't think double quotes are the issue, because I'm not entering a file path, just a workspace attribute (and I noticed none of the workspace attributes contain double quotes despite being strings).

    If this doesn't help could you share your workspace in FireCloud with [email protected]?"
    

    Done!

  • bshifawbshifaw moonMember, Broadie, Moderator admin

    What is the name of your workspace?

  • lraolrao Member
    edited July 2018

    fccredits-thulium-flax-2098/Germline-SNPs-Indels-GATK4-hg38

    If it helps, this one is the particular workflow that failed:

  • lraolrao Member

    Wow, that is a hard bug to spot. I just ran Mutect2 successfully, so that was the problem indeed!

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