"classifier does not support confidence values" with non-16S/18S data

Hi @Chris_Barrington,
This is not an issue specific to non-16S/18S data — it is almost always a formatting issue (we only encounter it when someone is compiling their own custom reference database). What marker gene are you looking at, by the way?

Most common issue: the taxonomies do not have equal numbers of ranks. You should make sure that each entry has the same number of ranks; if anything is missing species level, for example, just add an empty rank (‘s__’). Punctuation errors (e.g., missing semicolons) will also cause this issue.

Let me know if that helps you spot the problem! If not, we can help dig a little further…