@Nicholas_Bokulich and @BenKaehler, thank you so much for looking into this.
These data are 18S, so that would explain why the classification results are bad using green genes.
This is what I have done so far:
First of all, I imported my custom taxonomy and reference files, then I used these steps to make the classifier.qza:
qiime feature-classifier extract-reads --i-sequences Para_Oxy.qza --p-f-primer GCYGCGGTAATWCCAGCTCT --p-r-primer TGCNCTTCCGTCAATTYCTT --o-reads ref-seqs.qza
I have quite a bit of variability in my read length so I tried with and without putting the --p-trunc-len option, in both cases, I get the same error.
The funny thing is that when I use this same classifier with another set of data it works. But also when I use this ref-seqs.qza file for any other task works.
I really don't know what is going on and what I am doing wrong.
Attached the classifier.
Thank you so so much for helping me!
Francesca
classifier.qza (422.4 KB)