In the snp_allele_frequencies_advanced() and aa_allele_frequencies_advanced() functions, cohorts of samples with unassigned taxon can be formed if there are enough samples with "unassigned" taxon values.
This can occasionally manifest as test failures, e.g.:

Above the "ML-2_unas_2015" cohort has samples with unassigned taxon.
It would be better to exclude samples with unassigned taxon.