Hi @110147,
Looks like you are only receiving kingdom-level classifications. This is almost always an indication of human error, specifically whether the correct reference database or classifier was used. Please answer the following questions:
- What gene target/primers are you using?
- What classification method are you using? Please post the exact commands.
- I see that you are using greengenes. Did you use one of QIIME2’s pretrained classifiers or are you training your own classifier?
Chances are either:
- you are using a classifier trained with the wrong primers
- greengenes is not appropriate for your data. Are these bacterial 16S rRNA gene reads?
If you are receiving non-kingdom classifications, see this post for further troubleshooting.
I hope that helps!