Hi everyone,

I was trying to run ADMIXTURE using a merged vcf file with 82 samples. I pruned the data using a set of plink command:

plink --vcf 82_samples.vcf.gz --make-bed --double-id

plink --bfile 82_samples --indep-pairwise 50 5 0.5 --out 82_samples_pruned
plink --bfile plink --extract 82_samples_pruned.prune.in --make-bed --out 82_samples_pruned

Then I edited the.bim file ADMIXTURE does not accept chromosome names that are not human chromosomes usingan awk command:

awk '{$1=0;print $0}' 82_samples_pruned.bim > 82_samples_pruned.bim.tmp

After this, I ran ADMIXTURE using k=2,3,4,5 with a for loop:

for i in {2..5}; do admixture --cv 82_samples_pruned.bed $i > log${i}.out; done

But I'm geting a Segmentation Fault error.

The log file for k=2 has the following information:

ADMIXTURE Version 1.3.0
Copyright 2008-2015
David Alexander, Suyash Shringarpure,
John Novembre, Ken Lange


Please cite our paper!
Information at www.genetics.ucla.edu/software/admixture

Cross-validation will be performed. Folds=5.
Random seed: 43
Point estimation method: Block relaxation algorithm
Convergence acceleration algorithm: QuasiNewton, 3 secant conditions
Point estimation will terminate when objective function delta < 0.0001
Estimation of standard errors disabled; will compute point estimates only.
Size of G: 82x35511617

Can anyone help me?

Thanks in advance,

Pedro



Source link