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Mutect2 failure


I cloned the Somatic-SNVs-Indels-GATK4 workspace and I'm trying to run the 2-Mutect2_GATK4 workflow on several of my WES samples, which launched just under an hour ago. However, one of them has "failed" - I took screenshots on Terra to show what the error messages are (attached).

I'm hoping to get some guidance with respect to the source of the error, why it's showing up, and what can be done to prevent it. Thanks!!


Best Answers


  • aboyntonaboynton Member
    edited August 2019

    Thanks for the reply. I went to look that that error,

    And clicked on the folder icon which brought me to this script in the google bucket:

    cd /cromwell_root
    tmpDir=$(mkdir -p "/cromwell_root/tmp.62a83cf7" && echo "/cromwell_root/tmp.62a83cf7")
    chmod 777 "$tmpDir"
    export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
    export TMPDIR="$tmpDir"
    export HOME="$HOME"
    cd /cromwell_root
    out98a233ee="${tmpDir}/out.$$" err98a233ee="${tmpDir}/err.$$"
    mkfifo "$out98a233ee" "$err98a233ee"
    trap 'rm "$out98a233ee" "$err98a233ee"' EXIT
    tee '/cromwell_root/stdout' < "$out98a233ee" &
    tee '/cromwell_root/stderr' < "$err98a233ee" >&2 &
    cd /cromwell_root
    set -e
    export GATK_LOCAL_JAR=/root/gatk.jar
    # We need to create these files regardless, even if they stay empty
    touch bamout.bam
    touch f1r2.tar.gz
    echo "" > normal_name.txt
    gatk --java-options "-Xmx3000m" GetSampleName -R gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta -I gs://fc-4c00a50a-26eb-46ae-b5bd-095e1cfd7b6f/Bando_DIPG13_CellLine_WES_July2019/RP-924/Exome/DIPG13_pXPR051_sgPMS2_TMZ_100_3Months/v2/DIPG13_pXPR051_sgPMS2_TMZ_100_3Months.bam -O tumor_name.txt -encode
    tumor_command_line="-I gs://fc-4c00a50a-26eb-46ae-b5bd-095e1cfd7b6f/Bando_DIPG13_CellLine_WES_July2019/RP-924/Exome/DIPG13_pXPR051_sgPMS2_TMZ_100_3Months/v2/DIPG13_pXPR051_sgPMS2_TMZ_100_3Months.bam -tumor `cat tumor_name.txt`"
    if [[ ! -z "" ]]; then
        gatk --java-options "-Xmx3000m" GetSampleName -R gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta -I  -O normal_name.txt -encode
        normal_command_line="-I  -normal `cat normal_name.txt`"
    gatk --java-options "-Xmx3000m" Mutect2 \
        -R gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta \
        $tumor_command_line \
        $normal_command_line \
        --germline-resource gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf \
        -pon gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf \
        -L gs://fc-secure-d5c0365b-ea7d-406c-909c-e945da87288a/632b731f-d7fa-4b4c-a90c-e9a36739a70c/Mutect2/98a233ee-f6ac-4fd5-873a-76c17f4ef2dd/call-SplitIntervals/glob-0fc990c5ca95eebc97c4c204e3e303e1/0007-scattered.interval_list \
        -O "output.vcf" \
        --downsampling-stride 20 --max-reads-per-alignment-start 6 --max-suspicious-reads-per-alignment-start 6
    ### GetPileupSummaries
    # These must be created, even if they remain empty, as cromwell doesn't support optional output 
    touch tumor-pileups.table
    touch normal-pileups.table
    if [[ ! -z "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf" ]]; then
        gatk --java-options "-Xmx3000m" GetPileupSummaries -R gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta -I gs://fc-4c00a50a-26eb-46ae-b5bd-095e1cfd7b6f/Bando_DIPG13_CellLine_WES_July2019/RP-924/Exome/DIPG13_pXPR051_sgPMS2_TMZ_100_3Months/v2/DIPG13_pXPR051_sgPMS2_TMZ_100_3Months.bam --interval-set-rule INTERSECTION -L gs://fc-secure-d5c0365b-ea7d-406c-909c-e945da87288a/632b731f-d7fa-4b4c-a90c-e9a36739a70c/Mutect2/98a233ee-f6ac-4fd5-873a-76c17f4ef2dd/call-SplitIntervals/glob-0fc990c5ca95eebc97c4c204e3e303e1/0007-scattered.interval_list \
            -V gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf -L gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf -O tumor-pileups.table
        if [[ ! -z "" ]]; then
            gatk --java-options "-Xmx3000m" GetPileupSummaries -R gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta -I  --interval-set-rule INTERSECTION -L gs://fc-secure-d5c0365b-ea7d-406c-909c-e945da87288a/632b731f-d7fa-4b4c-a90c-e9a36739a70c/Mutect2/98a233ee-f6ac-4fd5-873a-76c17f4ef2dd/call-SplitIntervals/glob-0fc990c5ca95eebc97c4c204e3e303e1/0007-scattered.interval_list \
                -V gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf -L gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf -O normal-pileups.table
    )  > "$out98a233ee" 2> "$err98a233ee"
    echo $? > /cromwell_root/rc.tmp
    # add a .file in every empty directory to facilitate directory delocalization on the cloud
    cd /cromwell_root
    find . -type d -exec sh -c '[ -z "$(ls -A '"'"'{}'"'"')" ] && touch '"'"'{}'"'"'/.file' \;
    cd /cromwell_root
    mv /cromwell_root/rc.tmp /cromwell_root/rc

    I don't know enough to know whether the source of the error lies within that script.

    Thanks for your time!

    Post edited by bshifaw on
  • bshifawbshifaw Member, Broadie, Moderator admin

    In the folder icon are there any files called stdout or stderr? Or do you get sent to a file when you click on the paper icon with the red triangle?

  • aboyntonaboynton Member

    So, when I click on the stdout or stderr icons to the right of the error message

    I get brought to the google bucket "shard 7" folder but there's nothing there to read:

  • bshifawbshifaw Member, Broadie, Moderator admin

    Would we please share your workspace with [email protected] and share the name of your workspace so that we could take a closer look.

  • aboyntonaboynton Member

    I just shared it!

  • bshifawbshifaw Member, Broadie, Moderator admin

    Were you able to rerun the job, I see few other runs which look to be the same input file that succeeded? This maybe a transient error.

  • aboyntonaboynton Member

    Hey yep it seemed to work when I re-launched the analysis. That happened for a few other samples like you mentioned but they seem to work when I relaunch them. Are transient errors something to be worried about? Given it happened for a few samples I didn't know if it indicates some issue with the DNA being sequenced or something, the Mutect workflow, etc. Thanks!

  • aboyntonaboynton Member

    Okay thanks so much for your help!

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