Hi again @eDNA,
Another moderator chimed in with some helpful advice!
Have you dereplicated your reference database? Here is the rescript tutorial that may be helpful with that.
You could also skip the classifier and run feature-classifier classify-consensus-blast or feature-classifier classify-consensus-vsearch. For this you may want to consider setting either --p-maxaccepts 32 --p-maxrejects 128 or --p-maxaccepts 64 --p-maxrejects 256 as opposed to performing an exhaustive search.
Hope that helps!
