Hi everyone! This is my first time posting on this site, so hopefully I'm doing this right.
I am trying to validate a VCF file (containing variants from a mitochondrial genome) with GATK's ValidateVariants function. After running it, I don't necessarily get an error, but I got a few warnings that read:
Traversal complete. Processed 0 total variants in 0.0 minutes.
and
21:37:17.007 WARN IntelInflater - Zero Bytes Written : 0
21:37:17.013 WARN IntelInflater - Zero Bytes Written : 0
Does anyone know what this output means? Is there something wrong with my VCF file to cause this? Because the whole reason I am running this tool is to figure that out haha.
To me, it seems like nothing happened at all, and the program simply shut down without checking anything.
I checked my VCF file, but it is definitely not empty. I followed GATK's best practice steps for calling variants in a mitochondrial genome and none of the steps I took before this gave any errors. I do really want to make sure my VCF file is valid before continuing with my research, which is why I am hoping that there is someone who experienced this as well, and would be able to help me figure this out.
Thank you in advance!
please show us the full command line, the full message and the output of
gunzip -c /path/to/vcf.gz |grep -v "^#" |wc -l