I am attempting run ADMIXTURE and continue receiving a (new to me) error that I cannot seem to figure out:
Cross-validation will be performed. Folds=5. 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. zsh: abort ./admixture --cv pop.admix.bed 2
I have tried a couple of different vcf files to see if the file might be the issue, but it does not appear to be the specific file. I have also stripped my admixture command down to the bare essentials.
And, in case it is useful, the plink command I used to prep the files is:
./plink --vcf hapc.snps2.vcf.gz --make-bed --out pop.admix --allow-extra-chr --chr-set 38
I would appreciate any thoughts!