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Nothing happens when running GATK VCF Validate Variants. Output warning: processed 0 (zero) total variants

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!

gatk vcf snp validatevariants
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by maikejet • maikejet

please show us the full command line, the full message and the output of gunzip -c /path/to/vcf.gz |grep -v "^#" |wc -l

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written by Pierre Lindenbaum Pierre Lindenbaum

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