Taxonomy assignment output dosen't give full taxonomy even if its present in reference database

[Nicholas_Bokulich]

Welcome to the forum @vkk_24!

@vkk_24

Why does this happen even after giving a database which has all 7 level taxonomic annotation?

This is quite common and you already gave the answer:

@vkk_24

I totally understand it is difficult to get species/genus level annotation using only 16S sequences.

basically, some of your sequences are too short to differentiate those specific groups. It looks like for many of your sequences you are getting species-level classification, but for others you get phylum-level classification, because those query sequences are matching reference sequences from two or more different orders!

If you think there is a problem with the sequences, you can see this topic for some more details and troubleshooting:

Train you classifier - taxonomy

Hi @Jasmine84, See this post. Depending on the length of your sequences, the primers you are using, etc, deeper than order level might be unreliable. On 250 bp 16S rRNA gene sequences, we can usually get genus level and some species with a good degree of reliability. The naive bayes classifier in QIIME2 is designed to be cautious and reliable, to avoid false-positive errors, but you can lower the confidence parameter to make it less cautious. If you have: only kingdom-level classification, …

That's where I'd begin — look at the sequences that are underclassifying, since many of your classifications look good.