[Vcftools-help] VCF output file and log files don't reconcile

[Aisha Y. <ais...@ym...>]

Hi,
I ran vcftools on my example file using following command:
vcftools --gzvcf test.vcf.gz --remove-indels --min-alleles 2 --max-alleles 2 --recode --out test.bi.vcf
 It generates log file as well as output file. According to log info file doesn't contain any sites while I get out put file having "4633769" no. of sites.
Can you please figure out why log file and output file are not reconciling?
Thanks!
Log file is like this:
VCFtools - v0.1.13
(C) Adam Auton and Anthony Marcketta 2009Parameters as interpreted:
 --gzvcf test.vcf.gz
 --max-alleles 2
 --min-alleles 2
 --out test.bi.vcf
 --recode
 --remove-indelsUsing zlib version: 1.2.3
Versions of zlib >= 1.2.4 will be *much* faster when reading zipped VCF files.
After filtering, kept 1 out of 1 Individuals
Outputting VCF file...
After filtering, kept 4633769 out of a possible -1613936332 Sites
File does not contain any sites
Run Time = 40248.00 seconds