Vcftools Can'T Create Ped Map File Due To Ulimit Of Allowed Open Files.

Question

[Kevin]

I tried to generate the ped and map files but i ran into an error asking me to increase the number of allowed open files. But I can't seem to resolve this with ulimit.

Has anyone else run into this problem? or is the tped format good enough to create the .genome file for downstream analysis?

vcftools --gzvcf clean.chrY.vcf.gz --plink --out clean.chrY.vcf.gz.plinkformat

VCFtools - v0.1.9.0 (C) Adam Auton 2009

Parameters as interpreted: --gzvcf bybatch.clean.chrY.vcf.gz --out bybatch.clean.chrY.vcf.gz.plinkformat --plink

Using zlib version: 1.2.3 Versions of zlib >= 1.2.4 will be much faster when reading zipped VCF files. Reading Index file. File contains 162 entries and 3534 individuals. Applying Required Filters. After filtering, kept 3534 out of 3534 Individuals After filtering, kept 162 out of a possible 162 Sites Writing PLINK PED file ... Error:

Could not open temporary file.

Most likely this is because the system is not allowing me to open enough temporary files. Try using ulimit -n <int> to increase the number of allowed open files. Alternatively, try the --plink-tped command.

ulimit -n 4000 -bash: ulimit: open files: cannot modify limit: Operation not permitted

Answer 1

[Adam]

This is a limit imposed by your operating system. However, you could perhaps use the --plink-tped command instead of the --plink command, as this would require fewer temporary files?

Answer 2

[dweeks.pitt]

The Mega2 program can convert from VCF format to PLINK format.

See: http://watson.hgen.pitt.edu/docs/conversions/vcf_or_bcf_plink.html

Answer 3

[a.molkenov]

please try

ulimit -n 10000