Abnormal high percentage of unclassified bacteria

[SoilRotifer (Mike Robeson)]

Hi @Abdelhady_Elshal, welcome to :qiime2: !

If you search the forum, you find that the most common reason for this issue, is that your reads are in mixed orientation. Here is at least one thread that should help get you started:

train a greengenes 2022 classifier for forward reads only

Hi @mawa86, If the majority of your reads are being assigned as "Unassigned" and "k__Bacteria", it could mean that your reads are in a mixed orientation, with respect to the classifier. That is, the both the forward and reverse reads appear in the R1 files, and similarly, in the R2 files. You can read many forum threads about this here. One way to sanity-check if this is the case, is to run qiime feature-classifier classify-consensus-vsearch ... as vsearch does not care about read orientatio…