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PAPI error code 5. 10: Failed to delocalize files:

I launched an analysis using GATK Mutect2_pon method to create a panel of normals. This analysis has failed – I got a message regarding the error however I do not know how to fix it. There is a problem with copying .vcf and .vcf.idx files from a local disk to the google bucket associated with the workspace in which the analysis was performed.
I was wondering if I could share the workspace with [email protected] and ask you to have a look at the workspace/method configuration and to advise how to fix this error? Please provide me with your email address that I could use to share with you the submission and workflow ids as well as any other important details.

Thank you for your help!

Best Answer

Answers

  • bshifawbshifaw moonMember, Broadie, Moderator admin

    Hi @kklon

    We'd be happy to have a look at your issue. Once you've shared your workspace with [email protected] only users part of the FireCloud-Support team will be able to view the workspace. You can post your submission and workflow IDs here on this thread or message it to me on the gatkforums website by opening a link to my profile and then clicking message at the top right.

  • kklonkklon Member

    Great , thank you for your support @bshifaw ! I have already shared the workspace and sent you all the relevant details. Please let me know if you need any additional information.

  • bshifawbshifaw moonMember, Broadie, Moderator admin
    edited September 18

    Hi @kklon

    For this analysis I imported the method with configuration from the featured workspace 'help->gatk/Somatic-SNVs-Indels-GATK4'. I also uploaded most of the workspace attributes from this >workspace, despite intervals .bed file, which is a custom file specific for the WES analysis conducted in >Broad genomics platform, in which our data were generated.

    I was wondering if it is correct/efficient to use the GATK docker or should rather use another one?

    Feel free to use a smaller docker but I'd recommend sticking with the one we've provided. The provided docker image has all the necessary tools and the correct versioning to run the workflow.

    The steps used to check the error were written below, this may be helpful for future questions/problems.

    The stderr from your failed task has the following message

    ***********************************************************************
    
    A USER ERROR has occurred: Invalid argument 'Kwiatkowski_Everolimus_Trial_WES_PoN1.vcf'.
    
    ***********************************************************************
    

    So this message is from the gatk tool, and its complaining about the input.

    Now looking at the input provided to the workflow it looks like the normal bam and bai is empty, so perhaps there might be something wrong with the methods configurations

    Now checking the method configurations it looks like your using the same method configurations from the feature workspace.this.samples.bam and this.samples.bam_index

    However, looking through your data model it looks like your bam files are under the attribute (column) crai_or_bai_path and cram_or_bam_path

    Try changing the attribute name in the method configuration for normal bam and bai from this.samples.bam and this.samples.bam_index to this.samples.cram_or_bam_path and this.samples.crai_or_bai_path

    Let us know if this answers your questions.

    The following doc may help with trouble shooting terms: Troubleshooting in FireCloud

  • kklonkklon Member

    Hi @bshifaw,
    Thank you for your suggestion! It was helpful, during the newly launched analysis the normal_bais and normal_bams were localized properly in the inputs.
    However, this analysis (workflow id: 898866ec-a4fa-4099-8a1b-a0e62229f4ab ) also failed.

    I got again a similar error message, i.e.,:

    Task Mutect2.CalculateContamination:NA:1 failed. Job exit code 1. Check gs://fc-ac108ebf-b514-40e9-9aaf-e912285a7ba2/e89551b2-9729-4c5e-bcb9-88deeca842c1/Mutect2_Panel/898866ec-a4fa-4099-8a1b-a0e62229f4ab/call-Mutect2/shard-4/Mutect2/6a25d5ac-7fbc-4d18-81d3-8714b8135846/call-CalculateContamination/stderr for more information. PAPI error code 5. 10: Failed to delocalize files: failed to copy the following files: "/mnt/local-disk/pileups.table -> gs://fc-ac108ebf-b514-40e9-9aaf-e912285a7ba2/e89551b2-9729-4c5e-bcb9-88deeca842c1/Mutect2_Panel/898866ec-a4fa-4099-8a1b-a0e62229f4ab/call-Mutect2/shard-4/Mutect2/6a25d5ac-7fbc-4d18-81d3-8714b8135846/call-CalculateContamination/pileups.table (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/pileups.table gs://fc-ac108ebf-b514-40e9-9aaf-e912285a7ba2/e89551b2-9729-4c5e-bcb9-88deeca842c1/Mutect2_Panel/898866ec-a4fa-4099-8a1b-a0e62229f4ab/call-Mutect2/shard-4/Mutect2/6a25d5ac-7fbc-4d18-81d3-8714b8135846/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-ac108ebf-b514-40e9-9aaf-e912285a7ba2/e89551b2-9729-4c5e-bcb9-88deeca842c1/Mutect2_Panel/898866ec-a4fa-4099-8a1b-a0e62229f4ab/call-Mutect2/shard-4/Mutect2/6a25d5ac-7fbc-4d18-81d3-8714b8135846/call-CalculateContamination/contamination.table (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/contamination.table gs://fc-ac108ebf-b514-40e9-9aaf-e912285a7ba2/e89551b2-9729-4c5e-bcb9-88deeca842c1/Mutect2_Panel/898866ec-a4fa-4099-8a1b-a0e62229f4ab/call-Mutect2/shard-4/Mutect2/6a25d5ac-7fbc-4d18-81d3-8714b8135846/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-ac108ebf-b514-40e9-9aaf-e912285a7ba2/e89551b2-9729-4c5e-bcb9-88deeca842c1/Mutect2_Panel/898866ec-a4fa-4099-8a1b-a0e62229f4ab/call-Mutect2/shard-4/Mutect2/6a25d5ac-7fbc-4d18-81d3-8714b8135846/call-CalculateContamination/segments.table (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/segments.table gs://fc-ac108ebf-b514-40e9-9aaf-e912285a7ba2/e89551b2-9729-4c5e-bcb9-88deeca842c1/Mutect2_Panel/898866ec-a4fa-4099-8a1b-a0e62229f4ab/call-Mutect2/shard-4/Mutect2/6a25d5ac-7fbc-4d18-81d3-8714b8135846/call-CalculateContamination/segments.table, command failed: CommandException: No URLs matched: /mnt/local-disk/segments.table\nCommandException: 1 file/object could not be transferred.\n)"

    Additionally, in all three stedrr.log files (CalculateContamination_stedrr.log, CollectSequencingArtifactMetrics-stedrr.log and SplitIntervals-stedrr.log) I found such error

    "A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary"

    The alignment for all .bam files was performed using hg19 as a reference.
    Therefore, in my workspace attributes I am referring to the hg19 ref_dict, ref_fai and ref_fasta files, available at the gatk best practices workspace. I was wondering, however, if using exactly the same reference files that were used during the alignment might help or this error is referring to another issue?

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    Hi @kklon,

    As we haven't heard back from you in a few days, I will be marking Beri's answer as correct and closing this ticket. Please let us know if you are still encountering any FireCloud issues and we will be happy to take another look.

  • kklonkklon Member

    Yes, thank you @bshifaw and @KateN! I really appreciate your help!

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