classify-hybrid-vsearch-sklearn: Features Omitted from Taxonomy?

[Nicholas_Bokulich]

Hi @szymanski ,
Thanks for trying out this method. This is expected behavior, see here:

Classifier tool discard seqences that aren't found in reference database

Hello fellow qiimers! That's my first post here so I hope that it'll follow all community guidelines I'm using to perform 16S metagenomic analysis. Recently I wanted to review all possible options for classifying tools (been using vsearch classifier previously) and when I've tried to incorporate other commands from feature-classifier into my workflow I've received following error message from taxa barplot tool: Feature IDs found in the table are missing from the taxono…

@szymanski

While I could simply filter these features out of the table, some of them are abundant enough that I am hesitant to completely drop them.

Yes this is what should be done. These features are most likely non-target DNA (e.g., host DNA), which is why they are abundant but are filtered out due to non-alignment to the reference (< 60% similarity I think).

@szymanski

Is there a way to forcibly add these features to the extant taxonomy artifact?

You could create an artificial taxonomy for those features outside of QIIME 2, import, and then merge with the output of classify-hybrid-vsearch-sklearn.

@szymanski

Also, unfortunately, I am not able to access the debug info due to permissions on the system I am using. (Related: does the --output-dir option that is in most methods and plug-ins allow the redirection of debug info? its description is relatively vague)

No this cannot be redirected to the output directly, but you could run all commands with the --verbose flag, so that all messages are written to stdout.

Good luck!