We've moved!
You can find our new documentation site and support forum for posting questions here.

Mutect2 error

I tried to run the Mutect2 analysis, and this error happened:
Task Mutect2.CalculateContamination:NA:1 failed. Job exit code 1. Check gs://fc-8e19afa9-92cc-4f57-a6a2-4193fcf0f939/40a9b2ef-35be-4b7a-bbb7-14cab328459a/Mutect2/36013f64-7777-4630-b0ae-bffea2e708cf/call-CalculateContamination/CalculateContamination-stderr.log for more information. PAPI error code 5. Message: 10: Failed to delocalize files: failed to copy the following files: "/mnt/local-disk/pileups.table -> gs://fc-8e19afa9-92cc-4f57-a6a2-4193fcf0f939/40a9b2ef-35be-4b7a-bbb7-14cab328459a/Mutect2/36013f64-7777-4630-b0ae-bffea2e708cf/call-CalculateContamination/pileups.table (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/pileups.table gs://fc-8e19afa9-92cc-4f57-a6a2-4193fcf0f939/40a9b2ef-35be-4b7a-bbb7-14cab328459a/Mutect2/36013f64-7777-4630-b0ae-bffea2e708cf/call-CalculateContamination/pileups.table, command failed: CommandException: No URLs matched: /mnt/local-disk/pileups.table\nCommandException: 1 file/object could not be transferred.\n); /mnt/local-disk/contamination.table -> gs://fc-8e19afa9-92cc-4f57-a6a2-4193fcf0f939/40a9b2ef-35be-4b7a-bbb7-14cab328459a/Mutect2/36013f64-7777-4630-b0ae-bffea2e708cf/call-CalculateContamination/contamination.table (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/contamination.table gs://fc-8e19afa9-92cc-4f57-a6a2-4193fcf0f939/40a9b2ef-35be-4b7a-bbb7-14cab328459a/Mutect2/36013f64-7777-4630-b0ae-bffea2e708cf/call-CalculateContamination/contamination.table, command failed: CommandException: No URLs matched: /mnt/local-disk/contamination.table\nCommandException: 1 file/object could not be transferred.\n); /mnt/local-disk/segments.table -> gs://fc-8e19afa9-92cc-4f57-a6a2-4193fcf0f939/40a9b2ef-35be-4b7a-bbb7-14cab328459a/Mutect2/36013f64-7777-4630-b0ae-bffea2e708cf/call-CalculateContamination/segments.table (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/segments.table gs://fc-8e19afa9-92cc-4f57-a6a2-4193fcf0f939/40a9b2ef-35be-4b7a-bbb7-14cab328459a/Mutect2/36013f64-7777-4630-b0ae-bffea2e708cf/call-CalculateContamination/segments.table, command failed: CommandException: No URLs matched: /mnt/local-disk/segments.table\nCommandException: 1 file/object could not be transferred.\n)"

What can I do to fix and run the analysis?

Tagged:

Best Answer

Answers

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin
    edited May 2018

    The message is long, but the important part is at the beginning:

    Check gs://fc-8e19afa9-92cc-4f57-a6a2-4193fcf0f939/40a9b2ef-35be-4b7a-bbb7-14cab328459a/Mutect2/36013f64-7777-4630-b0ae-bffea2e708cf/call-CalculateContamination/CalculateContamination-stderr.log for more information. 
    

    If you are on the Monitor page for that run, you can scroll down to the Calls section and find CallCalculateContamination. Click Show, and then there should be a stderr log you can open. That should give you more information on what went wrong.

    If you'd like me to take a look, you can share the workspace in FireCloud with [email protected] I will also need you to share the following information here: Workspace name, Submission ID, and Workflow ID.

    Post edited by KateN on
  • Thank you for the response KateN. I did these steps to better understand how I managed this error, but I could not understand it very well. I'm going to share this Workspace with you, using the e-mail [email protected]

    You can contact me by the e-mail: [email protected]

    Thanks.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    Sorry, I do need the workspace shared in FireCloud itself (Workspace> Share button on the lefthand side), and then you can post the information about the workspace (Workspace name, Submission ID, and Workflow ID) here, or share it with me via direct message on the forum if you need to keep the information private.

  • I already did the workspace share, let me know if you received the share.
    The information are:
    Workspace name: giovanalgbm/Somatic-SNVs-Indels-GATK4_lgbm
    Submission ID: 40a9b2ef-35be-4b7a-bbb7-14cab328459a

    Sorry, but I can't found the workflow ID. Where can I find this information?

  • Ok KateN, thank you so much for the explanation and help. I saw in the other post how I can fix this problem. So, do you think that it's better I upload the unaligned BAM and run the analysis again?

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    My coworker tells me that everyone should use GRCh38, and it looks like your reads were already aligned to that one. You should keep your aligned bams and run this analysis using the GRCh38 reference.

Sign In or Register to comment.