Error: Too many distinct nonstandard chromosome/contig names.

[Becky Shaw]

Hi Christopher,

I am trying to learn to use plink to prune my variants for LD. 

I retrieved a VCF file from GATK that had been genotyped for snps from genomes of 49 non-model individuals. 

I have been following this tutorial to learn how to prune for snps from a vcf file: https://evomics.org/learning/population-and-speciation-genomics/2016-population-and-speciation-genomics/fileformats-vcftools-plink/

and have gotten stuck trying to convert my files to binary format.

this is the output from my log file:

PLINK v1.90b3w 64-bit (3 Sep 2015)

Options in effect:

  --allow-extra-chr

  --file all_samples_genotyped_snps1

  --make-bed

  --out all_samples_genotyped_snps1_out

Hostname: t128n16

Working directory: /ei/.project-scratch/6/61ea8b33-6b11-4e22-8ca7-67abbd719d07/mustelids/vcfs

Start time: Thu Feb  4 16:30:50 2021

Random number seed: 1612456250

128764 MB RAM detected; reserving 64382 MB for main workspace.

Error: Too many distinct nonstandard chromosome/contig names.

Any suggestions or help you can give me would be really appreciated.

Best wishes,

Rebecca

[Christopher Chang]

Update your plink 1.9 build.  The #-of-contigs limit was greatly increased in Feb 2016.