Running Mutect wdl on Cromwell
Hey, I've been trying to run wdl file (https://github.com/gatk-workflows/gatk4-somatic-snvs-indels/blob/master/mutect2_pon.wdl) for the Create somatic panel of normals workflow with the Cromwell executor. The input files for the workflow, as well as json and wdl file are present on the AWS instance from which I tried to run the Cromwell (version 53.1). The error message I got is:
Could not localize /mnt/.../Projects/.../Inputs/HG19_Broad_variant.fasta -> /home/.../cromwell-executions/Mutect2_Panel/.../call-Mutect2/shard-0/Mutect2/.../call-SplitIntervals/inputs/-.../HG19_Broad_variant.fasta:
/mnt/.../Inputs/HG19_Broad_variant.fasta doesn't exist
...
/mnt/.../Inputs/HG19_Broad_variant.fasta: Invalid cross-device link
/mnt/..../Inputs/HG19_Broad_variant.fasta -> /home/.../cromwell-executions/Mutect2_Panel/..../call-Mutect2/shard-0/Mutect2/0.../call-SplitIntervals/inputs/.../HG19_Broad_variant.fasta.tmp: No space left on device.
Fasta file (and it's indexes) is present on instance and it is listed in input json file. There is enough memory and space on the AWS instance.
Do you maybe have idea what could be an issue?
Thanks!
Milena
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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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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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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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