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.
So it sounds like one of your SNPs has all alleles missing, which is likely to happen if you've got only one genome there (yours).

You can remove SNPs that have missing alleles using plink

    plink --geno 0.1 --file your_file --recode --out your_filtered_file

geno 0.1 means 'remove variants with missing call rates exceeding the provided value (default 0.1)', 0.1 (10%) should be more than enough for your case since your missing rate is 1.0 (100%)

This should print how many SNPs have been filtered out.