I am trying to run this command on my vcf files:
vcftools --gzvcf LcovEx_africa.vcf.gz --maf 0.05 --out filtered.out
It seems to be working fine, however, it does not print out the output file but only the log file, please see below.
As I have been using these vcf files for several other purposes and utilities of the vcftools such as calculating Fst and it has been working fine, I am wondering what the problem could be here.
Thank you very much in advance for your help,
VCFtools - v0.1.11
(C) Adam Auton 2009
Parameters as interpreted:
Using zlib version: 188.8.131.52
Versions of zlib >= 1.2.4 will be *much* faster when reading zipped VCF files.
Reading Index file.
Building new index file.
Scanning Chromosome: 1
Writing Index file.
File contains 2550621 entries and 150 individuals.
Applying Required Filters.
Filtering sites by allele frequency and call rate
After filtering, kept 150 out of 150 Individuals
After filtering, kept 649848 out of a possible 2550621 Sites
Run Time = 1486.00 seconds