Hello,
I am sorry for the late response; I decided to confirm data uploads with my PI first.
Thank you for the suggestion to set --p-trim-left 0 instead. I tried this and it does seem to help a bit with overall classifications! I also omitted the other 3 'length parameter' settings too.
I still have features with confidence intervals slightly > 1 though. I'm attaching an example qzv file here.
The attached qzv file was classified with custom v1-v2 Greengenes reference, but all the feature classifier steps are the same as those I'd specified for Silva earlier 08b_01q3_ggCustomv1-v2Classifications.qzv (1.3 MB) .
Thanks again,
Jasmine