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Running Mutect wdl on Cromwell

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3 comments

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    Beri

    Hi Milena,

    Would it be possible to move all the input files to a location on the /home directory instead of the mounted directory then try re-running the workflow with paths corrected for in the json? 

    What is the disk specs for your instance, what's the output after entering "df -h"?

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    Milena Stanojevic

    Hey Beri,

    Thank you and sorry for the late reply.

    I had a successful run for the Mutect2 wdl workflow (https://github.com/gatk-workflows/gatk4-somatic-snvs-indels/blob/master/mutect2.wdl) using Cromwell (version 54) on Amazon instance, however I keep getting the errors for the Create Somatic Panel of Normals and the Normal-Normal wdl workflows with same input files.

    Input files for the workflow, as well as json and wdl files are present on the AWS instance from which I tried to run the Cromwell.

    Error message I got for the Create Somatic Panel of Normals this time is:

    USER ERROR has occurred: Failed to create reader from file:///mnt/.../Projects/.../cromwell-executions/Mutect2_Panel/.../call-Mutect2/shard-0/Mutect2/.../call-Filter/execution/merged-normal-filtered.vcf. 

    Error message I'm getting for the Normal-Normal workflow is the same as the one I was getting before:

    A USER ERROR has occurred: The specified fasta file (file:///mnt/.../Projects/.../Inputs/HG19_Broad_variant.fasta) does not exist.

    I tried moving inputs to the home directory as you suggested, but it is forbidden because there is not enough space.

    Instance metrics with "df -h" are:

    Filesystem     Size Used Avail Use% Mounted on
    udev        35G  0 35G 0% /dev
    tmpfs       6.9G 17M 6.9G 1% /run
    /dev/nvme0n1p1   9.7G 5.4G 4.3G 56% /
    tmpfs        35G  0 35G 0% /dev/shm
    tmpfs       5.0M  0 5.0M 0% /run/lock
    tmpfs        35G  0 35G 0% /sys/fs/cgroup
    /dev/loop1     29M 29M  0 100% /snap/amazon-ssm-agent/2012
    /dev/loop3     97M 97M  0 100% /snap/core/9804
    /dev/loop4     98M 98M  0 100% /snap/core/10444
    /dev/mapper/crypto 1008G 68G 889G 8% /mnt
    /dev/loop2     56M 56M  0 100% /snap/core18/1932
    /dev/loop5     33M 33M  0 100% /snap/amazon-ssm-agent/2996
    tmpfs       6.9G  0 6.9G 0% /run/user/200609
    tmpfs       6.9G  0 6.9G 0% /run/user/200568 (edited)

    Thank you again,

    Milena

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    Beri

    This gatk-workflows/gatk4-somatic-snvs-indels/ git repository has been archived, to obtain the latest version of the mutect workflow please visit the gatk repo

    I'm not familiar with the AWS but I'll help where i can. 

    1)For the first error 

    USER ERROR has occurred: Failed to create reader from file

    This might be associated with the gatk tool not having access the the input index file, can you confirm the merged-normal-filtered.vcf has an index stored in the same folder.

    2) "I tried moving inputs to the home directory as you suggested, but it is forbidden because there is not enough space." Would it be possible to move all the input/reference/workflow/cromwell executable to the mounted drive and executing the workflow from the mounted drive? 

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