Hi @Hillary_Smith,
Thanks for posting! And many thanks for checking out the other forum posts related to this issue first. I have a few questions to get started troubleshooting:
- What primers are you using?
- What is the length of the sequences that you are classifying?
- What types of samples are you analyzing? (just curious but it may be relevant here)
One way to test your classifier would be to classify a subset (10 would be enough) of the same sequences that you used to train the classifier. If you are still getting kingdom-level classifications, something is wrong with the classifier (or possibly the taxonomy format — I assume that you are using the QIIME-formatted UNITE dataset).
The best performance for UNITE would be achieved by training the classifier without extracting reference reads, using the “developer” version of the UNITE sequences. Thanks for already trying these different approaches! It gets us a bit closer to solving the problem…
Would you mind sending your classifier and query sequences so that I could examine these files? You can send as a direct message to me if you do not want to post these publicly on this forum.