note reason for inability to classify

As I see it, failure to classify a read/OTU at any given taxonomic rank could be due to either:

  • no sufficiently similar sequence in the classification database
  • several similar sequences in the classification database, but belonging to different taxa

Is there any way that it could be determined (& reported) upon which of these criteria a read fails to be classified?

You could look at the taxa that are descended from where your sequence classified to and see what you see.