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I/O error loading or writing tribble index file, ONLY on mounted folders (Ubuntu)
I am a bit stuck here. Any GATK tool I try (v3.5 and v3.7) that autocreates an index (e.g. ValidateVariants) fails in doing so with the following message:
MESSAGE: I/O error loading or writing tribble index file
However GATK correctly creates the vcf files (for example with UnifiedGenotyper) in the same folder.
- Manually creating/deleting/editing files in the same folder: No problem
- All folders have complete rw permissions for all users
- Copying the vcf file to a local drive and running ValidateVariants there correctly creates index file
- After the error message, the idx file exists but is empty
- Trying with different vcf files shows the same problem
- Both the GATK.jar and reference files are local, only the vcf file is on a mounted drive
So in summary, somehow GATK does not like my mounted drives, but only for creating indexes. I am on ubuntu 16.04. Will check source code now.