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.