Hello everyone! I'm trying to run TreeMix with conda. I first created a new environment and installed Treemix (conda install treemix -c bioconda -c conda-forge). The Treemix input file was created with the populations module from Stacks from a vcf with 894 SNPs from 6 populations. I tried running Treemix using the next command:
for M in {0..10};
do for k in 500 1000 1500;
do echo k \= $k;
treemix -i input.recode.p.treemix.gz -root OUT -m ${M} -k ${k} -bootstrap -o trmxout_${M}_${k};
done;
done
It seems to work since it rapidly outputs the files for M=0, but when it starts with the analysis for M=1, it takes forever. It's been 18 hours and it's still running the for M=1 with k=500. I've tried with only k=1500 and I think it finished cause it says
DONE.
But the prompt doesn't appear, so I don't think it really finished. I have runned TreeMix before and it never took that long, I don't know what may be the problem. Can someone please help me? Thank you.
UPDATE: It seems that if I try running without a "k" parameter (i.e. without specifying the number of bases between the evaluated SNPs) it works perfectly. Except with a very high "m" parameter, like 9 or more migration edges. I think that if I pre filtered my VCF for LD I might not need the k parameter, so the problem wouldn't matter anymore. But I don't know what was hapenning. Any thoughts?
