I had my whole genome sequenced. In plink, I put the VCF file through and it produced 3 files: plink.bed, plink.bim, and plink.fam. As recommended by Sam in another comment, I made a backup of plink.bim and ran this Linux command on the backup: "sed 's/^chrM\s/25\t/g; s/^chrX\s/23\t/g; s/^chrY\s/24\t/g; s/^chr//g' plink-backup.bim > plink.bim" With this the changes are reflected in the file plink.bim. I then run admixture "./admixture -j2 plink.bed 4" and I got this error:
Error: detected that all genotypes are missing for a SNP locus. Please apply quality-control filters to remove such loci.
I have no idea what to do at this point.