Question: Vcftools Can'T Create Ped Map File Due To Ulimit Of Allowed Open Files.
0
gravatar for Kevin
7.5 years ago by
Kevin630
Kevin630 wrote:

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

vcf vcftools ped plink • 7.5k views
ADD COMMENTlink modified 2.8 years ago by a.molkenov0 • written 7.5 years ago by Kevin630
2
gravatar for Adam
7.5 years ago by
Adam990
United States
Adam990 wrote:

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?

ADD COMMENTlink written 7.5 years ago by Adam990
0
gravatar for dweeks.pitt
5.4 years ago by
dweeks.pitt40
United States
dweeks.pitt40 wrote:

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

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

ADD COMMENTlink written 5.4 years ago by dweeks.pitt40
0
gravatar for a.molkenov
2.8 years ago by
a.molkenov0
a.molkenov0 wrote:

please try

ulimit -n 10000

ADD COMMENTlink written 2.8 years ago by a.molkenov0
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