Thanks for the info about filtering in QIIME 2! I'll definitely move to that.
Here's the new command (without the Combo column):
qiime diversity beta-group-significance \
--i-distance-matrix core-metrics-results-CyanoOnly/bray_curtis_distance_matrix.qza \
--m-metadata-file New-metadata.tsv \
--m-metadata-category Site \
--o-visualization core-metrics-results/Bray_Curtis_Combo.qzv \
--p-pairwise
Also, here's the exact error:
Plugin error from diversity:
All values in the grouping vector are unique. This method cannot
_ operate on a grouping vector with only unique values (e.g., there are
_ no 'within' distances because each group of objects contains only a_
_ single object)._
Debug info has been saved to /tmp/qiime2-q2cli-err-6m2v3t8l.log.
Metadata columns with only two options work, so if the Site column only has "Sandy" or "Silty" it will work but not with multiple different values (even though the different values each have more than one instance).
Thanks for the info about the metadata table setup!