Only kindom level after taxonomic assigment

[Elav90 (Valeria)]

Hi everyone! I`m new with qiime2. I have read from Illumina Miseq. i worked in qiime1 until the demultiplexing steps. Then I imported my fna file in qiime 2 and I try to run the taxonomic assignement step with this command:
qiime feature-classifier classify-sklearn --i-classifier gg-13-8-99-515-806-nb-classifier.qza --i-reads rep-seqs_plate1.qza --o-classification taxonomy.qza
the script runs but the problem is that I have only the kindgom classification.

How can I resolve that?
thanks
Regards

[Nicholas_Bokulich]

Hi @Elav90,
See this post:

Classifier just class level

Hi @110147, Looks like you are only receiving kingdom-level classifications. This is almost always an indication of human error, specifically whether the correct reference database or classifier was used. Please answer the following questions: What gene target/primers are you using? What classification method are you using? Please post the exact commands. I see that you are using greengenes. Did you use one of QIIME2’s pretrained classifiers or are you training your own classifier? Chances a…

Kingdom-level classification is usually a result of using the incorrect reference database (or the wrong query sequences for that matter).

@Elav90

--i-classifier gg-13-8-99-515-806-nb-classifier.qza

Are you using the same primers? (515f/806r for 16S rRNA genes)

Please give us some more details and we can help solve this!

[Elav90 (Valeria)]

thank for the quickly answer. I used the primers 515F and 926R for 16S rRNA genes.
How can I build a correct database?

thanks so much!

Valeria

[Nicholas_Bokulich]

@Elav90

I used the primers 515F and 926R for 16S rRNA genes.

Yep! That's the problem. You can either:

1. Train your own classifier following these instructions (substitute your primers in the extract-reads step)

OR

2. Use one of the full-length 16S pre-trained classifiers.

Good luck!