Errors for MuTect2_pon: CalculateContamination

Hi GATK team,

Hope you are doing well! When I used mutect2_pon to generate the PON for my normal samples, an error shows up as follows:

Task Mutect2.CalculateContamination:NA:1 failed. Job exit code 1. Check gs://fc-55cfa650-ed51-40b9-bf5b-0ffce25419a8/f672323d-abbd-421f-a0e4-0a0b9cd1376a/Mutect2_Panel/715ece9a-5190-4e05-bd23-08ff6c70a553/call-Mutect2/shard-0/m2.Mutect2/7d48d9a6-5021-470a-9f81-0eb4818dfbe0/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-55cfa650-ed51-40b9-bf5b-0ffce25419a8/f672323d-abbd-421f-a0e4-0a0b9cd1376a/Mutect2_Panel/715ece9a-5190-4e05-bd23-08ff6c70a553/call-Mutect2/shard-0/m2.Mutect2/7d48d9a6-5021-470a-9f81-0eb4818dfbe0/call-CalculateContamination/pileups.table (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/pileups.table gs://fc-55cfa650-ed51-40b9-bf5b-0ffce25419a8/f672323d-abbd-421f-a0e4-0a0b9cd1376a/Mutect2_Panel/715ece9a-5190-4e05-bd23-08ff6c70a553/call-Mutect2/shard-0/m2.Mutect2/7d48d9a6-5021-470a-9f81-0eb4818dfbe0/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-55cfa650-ed51-40b9-bf5b-0ffce25419a8/f672323d-abbd-421f-a0e4-0a0b9cd1376a/Mutect2_Panel/715ece9a-5190-4e05-bd23-08ff6c70a553/call-Mutect2/shard-0/m2.Mutect2/7d48d9a6-5021-470a-9f81-0eb4818dfbe0/call-CalculateContamination/contamination.table (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/contamination.table gs://fc-55cfa650-ed51-40b9-bf5b-0ffce25419a8/f672323d-abbd-421f-a0e4-0a0b9cd1376a/Mutect2_Panel/715ece9a-5190-4e05-bd23-08ff6c70a553/call-Mutect2/shard-0/m2.Mutect2/7d48d9a6-5021-470a-9f81-0eb4818dfbe0/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-55cfa650-ed51-40b9-bf5b-0ffce25419a8/f672323d-abbd-421f-a0e4-0a0b9cd1376a/Mutect2_Panel/715ece9a-5190-4e05-bd23-08ff6c70a553/call-Mutect2/shard-0/m2.Mutect2/7d48d9a6-5021-470a-9f81-0eb4818dfbe0/call-CalculateContamination/segments.table (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/segments.table gs://fc-55cfa650-ed51-40b9-bf5b-0ffce25419a8/f672323d-abbd-421f-a0e4-0a0b9cd1376a/Mutect2_Panel/715ece9a-5190-4e05-bd23-08ff6c70a553/call-Mutect2/shard-0/m2.Mutect2/7d48d9a6-5021-470a-9f81-0eb4818dfbe0/call-CalculateContamination/segments.table, command failed: CommandException: No URLs matched: /mnt/local-disk/segments.table\nCommandException: 1 file/object could not be transferred.\n)"

Then when I checked the error file of task Mutect2.CalculateContamination, I saw something as follows.

A USER ERROR has occurred: Traversal by intervals was requested but some input files are not indexed.
Please index all input files:

samtools index /5194b788-527c-4f75-af31-8c86aa4fb40e/picardRealignment_indel/78ac03be-523b-4fd4-93bf-ede14b7b47ef/call-indelRealigner/attempt-4/glob-cac2c0609a22bf6a2708647f01ae757c/084normal.sorted084.bam

However, I've fed the index file at the very beginning to the workflow mutect2.pon, so I am not quite sure what's going on here. I also checked the codes inside Mutect2.CalculateContamination, and it seems like there's no input attribute for bam index file.

call CalculateContamination {
input:
gatk_override = gatk_override,
intervals = intervals,
ref_fasta = ref_fasta,
preemptible_attempts = preemptible_attempts,
max_retries = max_retries,
gatk_docker = gatk_docker,
tumor_bam = tumor_bam,
normal_bam = normal_bam,
variants_for_contamination = variants_for_contamination,
disk_space = tumor_bam_size + normal_bam_size + ceil(size(variants_for_contamination, "GB") * small_input_to_output_multiplier) + disk_pad
}

Any helps would be appreciated! Thanks!

Regards,
Z

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