A USER ERROR has occurred: Badly formed genome unclippedLoc

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suzy_bunters

• March 24, 2021 09:43

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.0.10.1  
b) Exact command used:

 gatk --java-options "-Xmx4G -XX:+UseParallelGC -XX:ParallelGCThreads=2" HaplotypeCaller \
-R trimmed.fasta \
-I ${sampleName}_trim_RG.bam \
-O ${sampleName}.g.vcf.gz \
-XL ${listName} \
-ERC GVCF \
-G StandardAnnotation \
-G AS_StandardAnnotation

c) Entire error log:

A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "Chr13 1 3456616" is not valid for this input.  

Hi there, 

I've checked the other posts with this error but none seem to solve my problem. 

HaplotypeCaller runs with no errors with this exact command, minus the -XL command.  

The file `listName` is named `sample_name.list` and contains 13 lines. The first 12 lines have chromosome names (Chr1 etc.) and the final line has "Chr13 1 3456616" separated by spaces (I've also tried tab delimited).

The documentation https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists states that the file can be named .list or .intervals and that Both <chr> <start> <stop> and <chr> can be present in the same file. I've also tried naming the file .intervals and .interval_list but that doesn't work either. 

Any help would be much appreciated! 

Kind regards

Suzanne 

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  Genevieve Brandt (she/her)

  • March 24, 2021 15:02

  Hi suzy_bunters,

  Could you try only specifying that interval in the -XL parameter in the format chr20:1-100? To check if the issue is with the interval or the submitted format.

  Genevieve

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  suzy_bunters

  • March 25, 2021 09:14

  Hi Genevieve, it's now running in the format you suggested, thank you. Each job I submit to the cluster sits in a queue for hours, so testing different formats was taking a long time! 

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  Genevieve Brandt (she/her)

  • March 25, 2021 14:59

  Hi suzy_bunters, if that runs fine, then the issue must be with the format of the file. For a workaround, you can submit the file without that line and then use another -XL argument to use the format I recommended above. It is fine to submit multiple interval arguments.

  Best,

  Genevieve

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