GATK mutect2 failing on gnomad input size determinatino

ekofmanekofman Member, Broadie

Hi,

I am running GATK's mutect2 on FireCloud. I am using the value "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf‎" for the attribute gnomad. I am receiving this failure 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-b37/af-only-gnomad.raw.sites.vcf‎

Is this a known issue? Any help much appreciated, thanks.

-Eric

Best Answer

Answers

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @ekofman we are looking into this now and will report back.

  • bshifawbshifaw Member, Broadie, Moderator admin
    edited June 2018

    Hi ekofman,

    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.

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

    Post edited by Tiffany_at_Broad on
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