Hi Matthew,
Thanks for your help. I really appreciate it.
Based on the suggested posts and this one I tried to use a full-length classifier (by skipping qiime feature-classifier extract-reads) and I got the same results:
I also tried different databases, GG vs. SILVA, still the same strange results.
I tried SILVA_97 vs SILVA_99, still the same.
I tried pre-trained classifier vs. my-trained classifier, the same results.
Some time ago I run qiime1 with the same datasets and I didn't observe such results. That is why I thought it has to do something with the classification.
Just to check I chose randomly one unclassified sequence and one Bacteria__ sequence and I put them into BLAST and SILVA_db, and there I am getting a taxonomic classification.
E.g. Here are the BLAST results for Bacteria__:
and here for SILVA:
So I wonder, why I do not see any assigned classification when using qiime2. Any idea?
Many thanks,
Joanna