bait_set_name in WGS DRAGEN-GATK pipeline

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NawarDalila

• January 14, 2022 08:47
• Edited

Hi,

I am running the DRAGEN-GATK pipeline on our HPC and it is failing with this error:

Failed to evaluate input 'references' (reason 1 of 1): Error(s):
No value for field 'evaluation_interval_list' with non optional type 'File' has been provided
No value for field 'bait_set_name' with non optional type 'String' has been provided
Required workflow input 'wgs.wgs_coverage_interval_list' not specified

I tried to look up the two missing files and I couldn't locate any of them in the GATK resource bundle for hg38. The closest was a file called wgs_calling_regions.hg38.interval_list "calling_interval_list". Can I use it for the missing ones as well?

Also, I don't know if the 'bait_set_name' argument is just an arbitrary name that I can use or is it something I should think about it? In anyway it is not inside your input file for the pipeline.

Thanks in advance for your help

Nawar

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• 

  Genevieve Brandt (she/her)

  • January 20, 2022 17:38

  Hi NawarDalila,

  After I helped with the other post, did you have any success with this error regarding the interval list?

  If you are still having issues with this problem, could you clarify your question further? Please include what exactly you are running. 

  Best,

  Genevieve

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