Hi,
I'm running Mac OS Mojave and I've encountered an error trying to run TreeMix.
ERROR: cannot open file treemix.freq.gz
Here are the steps I have used:
Convert .vcf file to plink format (ped):
vcftools --vcf data.vcf --plink --out data
Convert to binary format (bin bam bed):
plink --file data --noweb --make-bed --recode --missing-genotype 0 --out data
Make and stratified plink file Edit the .fam file and write the population names in the third column and save as cluster file
plink --bfile data --freq --missing --within data.clust --noweb
OR
plink --bfile data --write-cluster --family
Edit clust file and place population names in the third column
plink --bfile data --freq --missing --within data.clst --noweb
zip file
gzip plink.frq.strat
use python script to convert to treemix file
plink2treemix.py plink.frq.strat.gz treemix.frq.gz
TreeMix:
treemix -i treemix.freq.gz -o out_stem
# ERROR: cannot open file treemix.freq.gz
I feel like this might be an issue with zipping on Mac? As, all the datafiles appear to be fine.