Only kindom level after taxonomic assigment

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?

Hi @Elav90,
See this post:

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

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

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

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!


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

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


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

Good luck!


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