I was having trouble testing the feature-classifier that I have generated through following “Training feature classifier tutorial”(https://docs.qiime2.org/2018.6/tutorials/feature-classifier/)
V3 and V4 of 16S sequence were extracted from the SILVA full-length database using the f/r primer sequences given by the sequencing facility. Below was the script I used.
qiime feature-classifier extract-reads
Classifier was trained as below:
qiime feature-classifier fit-classifier-naive-bayes
And the classifier was tested using my 16S dataset of 17 samples (testset):
qiime feature-classifier classify-sklearn
qiime metadata tabulate
When done, I viewed the taxonomy.qzv file and it gave me the same taxon for all 1606 of my feature IDs:
D_0__Archaea;D_1__Nanoarchaeaeota;D_2__Nanoarchaeia;D_3__Nanoarchaeales;D_4__Nanoarchaeaceae;D_5__Nanoarchaeum;D_6__hot springs metagenome
What may have caused this?
- I’ve checked to see if the classifier.qza file was wrong by using the rep-set.qza file from the “MovingPictures tutorial”, and it seemed fine (various taxons were listed)
- I’ve visualized the rep-set.qzv, table.qzv and denoising-stats.qzv files but none of them show one single feature.
Thanks in advance for the help.