[Vcftools-help] vcf to plink individual limit

[Richard S. <sm...@eb...>]

Hi
I am try to convert a vcf file with genotypes for 1525
individuals into plink format. Is there a memory limit
for the number of individuals that can be processed ?

Trying to run a test on 1 line of the vcf gives error

vcftools_0.1.5/cpp/vcftools --plink --vcf try1000.vcf --out fred

VCFtools - v0.1.5
(C) Adam Auton 2009

Parameters as interpreted:
         --out fred
         --plink
         --vcf try1000.vcf

Scanning try1000.vcf ...
Currently scanning CHROM: 1
         Keeping 1 entries (out of 1 read)
Done
Kept 1525 out of 1525 Individuals
Kept 1 out of 1 Sites
Writing PLINK PED file ... Error:Could not open temp file.

===
Reducing individuals to 1019
cut -f 1-1028 try1000.vcf > test.vcf

VCFtools - v0.1.5
(C) Adam Auton 2009

Parameters as interpreted:
         --out fred
         --plink
         --vcf test.vcf

Scanning test.vcf ...
Currently scanning CHROM: 1
         Keeping 1 entries (out of 1 read)
Done
Kept 1019 out of 1019 Individuals
Kept 1 out of 1 Sites
Writing PLINK PED file ... Error:Could not open output file: fred.ped
=======

Reducing individuals to 1018 works.
cut -f 1-1027 try1000.vcf > test.vcf

vcftools --plink --vcf test.vcf --out fred

VCFtools - v0.1.5
(C) Adam Auton 2009

Parameters as interpreted:
         --out fred
         --plink
         --vcf test.vcf

Scanning test.vcf ...
Currently scanning CHROM: 1
         Keeping 1 entries (out of 1 read)
Done
Kept 1018 out of 1018 Individuals
Kept 1 out of 1 Sites
Writing PLINK PED file ... Writing PLINK MAP file ... Done.
Run Time = 0.00 seconds


the vcftools code used was downloaded today.

The vcf file passes the vcftool validator.

Thanks.

-- 
Richard Smith
DCC 1000 Genomes Project
European Bioinformatics Institute