vcftools not outputting any file, and not giving any error message

Question

[dec986]

Hello,

I'm running this vcftools command on a 148 GB vcf.gz flie:

nohup vcftools --exclude-positions X.bed --gzvcf merged.vcf.gz --out merged.noX &

the bed file was made with vcf2bed.

however, even after about 15 minutes, there is no output except a log file, and the program keeps running.

the log file shows:

VCFtools - 0.1.17
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --gzvcf merged.vcf.gz
    --exclude-positions X.bed
    --out merged.noX

Using zlib version: 1.2.7
Warning: Expected at least 2 parts in FORMAT entry: ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1">
After filtering, kept 2501 out of 2501 Individuals

Did I do anything wrong? Why isn't this making any output file? Or should I just wait?

Even if I re-direct output to STDOUT, I get nothing.

I'm anxious, because this could take a long time to run, and I don't want to waste hours of time for some minor mistake.

Answer 1

[dec986]

the problem was that vcftools needs recode to have output at all.

vcftools --exclude-positions X.bed --gzvcf merged.vcf.gz --out merged.noX --recode