EOF marker absent in VCF

EOF marker absent in VCF – can this be safely ignored?



I generated a VCF file using a bcftools mpileup | bcftools call pipeline. I have done this before, and the file produced then looks fine. However, the log for this one had

[W::bgzf_read_block] EOF marker is absent. The input is probably truncated

but the job ran to successful completion anyway (I have an echo at the end of my job script that is only reached if all previous lines exit with exit code 0 – set -eo pipefail, so I am sure every preceding line ran suceesfully). Does this mean this warning can safely be ignored and will not cause any problems in the future?

I ask because a subsequent operation failed and this Warning was shown again with an Error that I cannot reproduce (I will create a new post for that an update the content here with a link)

EDIT: Here is the link to the other connected question: Error while subsetting VCF – error doesn’t check out with (z)grep





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