Admixture error in removing loci with no genotypes even after filtering loci

Question

[Whirlingdaf]

I am attempting to run ADMIXTURE on plink derived .bed files and continue to get the error

Error: detected that all genotypes are missing for a SNP locus.
Please apply quality-control filters to remove such loci.

I have already performed multiple quality control steps prior to this point. E.g:

Filtered my vcf to: keep variants that have been successfully genotyped in 20% of individuals, a minimum quality score of 10, and a minor allele count of 3

vcftools --gzvcf bcftools_merged.vcf.gz --max-missing 0.2 --mac 3 --minQ 10 --recode --recode-INFO-all --out bcftools_filtered

Apply a minimum depth for genotypes:

vcftools --vcf bcftools_filtered.vcf --minDP 10 --recode --recode-INFO-all --out bcftools_filtered2

Then work with plink to create bed files and filter for LD as recommended in the tutorial:

plink --vcf bcftools_filtered2.vcf --make-bed --out bcftools_filtered2 --allow-extra-chr --chr-set 38
plink --bfile bcftools_filtered2 --indep-pairwise 50 10 0.1 --allow-extra-chr --chr-set 38
plink --bfile bcftools_filtered2 --extract plink.prune.in --make-bed --out prunedData --allow-extra-chr --chr-set 38

As I also have a number of non-numeric scaffolds, I need to remove these before running ADMIXTURE:

awk '{$1="0";print $0}' prunedData.bim > prunedData.bim.tmp
mv prunedData.bim.tmp prunedData.bim

And finally, attempt to run Admixture:

for K in 2 3 4 5 6 7 8 9 10; do admixture --cv prunedData.bed $K -j6 | tee log${K}.out; done

Which still returns the error:

Cross-validation will be performed.  Folds=5.
Parallel execution requested.  Will use 6 threads.
Random seed: 43
Point estimation method: Block relaxation algorithm
Convergence acceleration algorithm: QuasiNewton, 3 secant conditions
Point estimation will terminate when objective function delta < 0.0001
Estimation of standard errors disabled; will compute point estimates only.
Error: detected that all genotypes are missing for a SNP locus.
Please apply quality-control filters to remove such loci.

I would truly appreciate any assistance, I am running out of ideas to trouble shoot this.

Thank you!