I am trying to run and benchmark the GATK five-dollar-genome pipeline.
I ran the pipeline with the same parameters as this JSON file within the GitHub repo. However, the pipeline failed on the BaseRecalibrator tasks. I checked the log file for these tasks and it contained the following:
A USER ERROR has occurred: Cannot read /cromwell_root/broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx because no suitable codecs found
The index file being used is gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx and so shouldn't be causing any issues. Also, I have shared this workspace with GROUP_FireCloud-Support@firecloud.org.
Any ideas what the issue is and how it can be resolved?
Thanks in advance
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