difficulty understanding taxon assignment

Hello everybody, I get my ASV table with qiime2 (qiime feature-classifier classify-sklearn) and SilvaDatabase (silva-138-99-nb-classifier.qza), but checking this table I found some ASVs with controversial taxon names. Lines below, you will see that, for example: ASV1, ASV2 and ASV3 were classified as g__Lentimicrobiaceae, however Lentimicrobiacea is not a valid name for genus level, but family level.

Interestingly, a valid genus name (Lentimicrobium) was assigned only for ASV4. Any idea what is going on? is it a issue because of "qiime feature-classifier classify-sklearn" or by Silva Database?

ASV1. 4ff80dfc51c14558f15c3c3f175cdd0c|d__Bacteria| p__Bacteroidota| c__Bacteroidia| o__Sphingobacteriales| f__Lentimicrobiaceae| g__Lentimicrobiaceae| s__wastewater_metagenome

ASV2. fcf57ee73ef6cb269643c4cf02cd53d1|d__Bacteria| p__Bacteroidota| c__Bacteroidia| o__Sphingobacteriales| f__Lentimicrobiaceae| g__Lentimicrobiaceae

ASV3. 3b64ae26c096450fc67b592a4ce5ede8|d__Bacteria| p__Bacteroidota| c__Bacteroidia| o__Sphingobacteriales| f__Lentimicrobiaceae| g__Lentimicrobiaceae

ASV4. a2d8e8a630a0ab347f8f93a090f9a0fb|d__Bacteria| p__Bacteroidota| c__Bacteroidia| o__Sphingobacteriales| f__Lentimicrobiaceae| g__Lentimicrobium

I will appreciate any help. Thanks!

Hi @Peter_Janampa ,

Neither, but more the SILVA database. See here:

Note, if you really want to you can follow the tutorial at that link to create your own pre-trained classifier and turn off the rank propagation option... or you can just ignore the propagated ranks now that you know why they are there :grin:


Thank you so much, Nicholas!!!

I will read with more detail that link...but so far I understand that this is a "propagation rank issue".
I was wondering to "clean" manually this propagated ranks since I want to work with only genus level. Now I have a good justification to make this "cleaning".

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No need to clean manually... you can just build your own classifier with the propagation option switched off. Or you could use qiime rescript edit-taxa to edit the taxonomy based on a pattern (e.g., search and remove the propagated ranks that you do not want).


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