issue with gatk4-exome-analysis-pipeline when running given sample data
- /opt/gatk_workflow/WF_ID/cromwell-executions/ExomeGermlineSingleSample/9278f766-f409-4c1d-9edd-5c1cda167fd0/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/a08beb5f-6e60-4db0-9999-0532ccff675f/call-BaseRecalibrator/shard-13/execution/stderr.
- above showing error during baseRecalibrator
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A USER ERROR has occurred: Traversal by intervals was requested but some input files are not indexed.
Please index all input files:samtools index /cromwell-executions/ExomeGermlineSingleSample/9278f766-f409-4c1d-9edd-5c1cda167fd0/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/a08beb5f-6e60-4db0-9999-0532ccff675f/call-BaseRecalibrator/shard-13/inputs/-2087375849/HG00133.GRCh38DH.exome.aligned.duplicate_marked.sorted.bam
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pipeline is not able to create imdex file using samtools and after that during re-calibration its expecting index which is not present so resulting in workflow failed
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is there any way to resolve this
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Hi Umang,
Happy to see if I can help here. Am I correct in understanding that you are running this on a personal Cromwell?
Can you provide a link to the workflow you are using? Can you also provide the .log, stdout, and stderr files for your job?
Many thanks,
Jason -
Hi Jason ,
It worked , we have made changes in UnmappedBamToAlignedBam.wdl and BamProcessing.wdl by adding "input_bam_index" variable and its file location
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Hi Umang,
Glad to hear it worked!
Kind regards,
Jason
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I was able to reproduce this and have made a PR.
https://github.com/gatk-workflows/gatk4-exome-analysis-pipeline/pull/18
Thanks for the good reporting umang kumar !
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Hi, I am having the same issue and getting the same error at the same step with the gatk4-genome-processing-pipeline. I am new to running GATK workflows and don't understand how to implement your solution.
Where do you add "input_bam_index and the file location"? Any details regarding how you fixed the error would be greatly appreciated.Best,
Grace
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Hi Grace,
GATK have made changes in there repository .Take the latest build .
I got mail from them stating they identified the bug and made the changes.
if not i mentioned the file name declare it in variable section.Regards
Umang
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