ADMIXTURE haploid mode does not converge

Question

[samuelandjw]

I'm trying to reproduce the results (Table 1) described in Shringarpure et al. - 2016 - Efficient analysis of large datasets and sex bias

The results involved calculation of global admixture proportions on the X chromosomes of both male and female samples, using the newly introduced "haploid" mode. I downloaded the chrX genotypes in PLINK1 format from here. I filtered the genotypes as described in the paper, by removing SNPs with MAF<0.05 and LD thinning pairs of SNPs with r^2<0.1. After that, I ran ADMIXTURE haploid mode using option --haploid=“male:23”. However, the run had not converged after >100 iterations.

This is the script I ran ADMIXTURE:

plink --bfile  1kg_phase1_chrX \
        --memory 2000 \
        --maf 0.05 \
        --make-bed \
        --out chrX.maf_0.05

plink --bfile chrX.maf_0.05 \
        --indep-pairwise 50 5 0.1

plink --bfile chrX.maf_0.05 \
        --extract plink.prune.in \
        --make-bed \
        --out chrX.filtered \

admixture --haploid="male:23" -s 1 chrX.filtered.bed 2 -j 12

Looking at the log files, it seems that ADMIXTURE had a hard time in finding a local maximum:

276 (QN/Block)  Elapsed: 1.811  Loglikelihood: -8.52897e+06     (delta): 1.42774  
277 (QN/Block)  Elapsed: 1.602  Loglikelihood: -8.52881e+06     (delta): 156.512 
278 (QN/Block)  Elapsed: 1.685  Loglikelihood: -8.52891e+06     (delta): -99.4092 
279 (QN/Block)  Elapsed: 1.618  Loglikelihood: -8.52884e+06     (delta): 68.4685 
280 (QN/Block)  Elapsed: 1.653  Loglikelihood: -8.52883e+06     (delta): 12.983 
281 (QN/Block)  Elapsed: 1.697  Loglikelihood: -8.52894e+06     (delta): -110.379

What did I do wrong?

Answer 1

[samuelandjw]

After communications with experts in the filed, it seems that there is bug with ADMIXTURE when both --haploid and -j (multi-threading flag) are used at the same time. Using --haploid without using -j solves the problem.