Hello guys, this is my first post in the forum.
I have been a great fan of QIIME2 and its plugins.
I followed exactly this tutorial to download and train a classifier based on the NCBI RefSeq 16S rRNA data. The resulting classifier looks fine according to the evaluation and predicted-taxonomy outputs. However, when I used this classifier to classify my own data, which are 16S rRNA sequences spanning the V1-V9 region sequenced using PacBio, it gave me some weird results (see below).
The sequences themselves shouldn't be the culprit because the same dataset classified using a classifier trained on SILVA full-length 16S rRNA sequences gave me reasonable results (see below).
Any idea what had gone wrong here? Thanks!