Dear Qiime 2 help desk,
I met a strange problem using a UNITE ITS-trained classifier in Qiime 2, i.e. some sequences are classified with significantly lower resolutions if they are submitted with other sequences than that they are submitted alone!
I picked up two sequences to make a very simple example:
When individually submitted, they were both classified as: k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__Tremellales;f__Tremellaceae;g__Cryptococcus;s__Cryptococcus_neoformans
However, sequence “123830878d97229ae38d4d57ca68335c” was classified as “k__Fungi” when these two sequences were submitted to the classifier together!
I would greatly appreciate if you would help to run the UNITE classifier on these two sequences and to see if the same observations can reproduced. Thank you so much!
I am using qiime2-2019.4. The following were what I did:
I downloaded a 2017 UNITE reference set from (wget https://files.plutof.ut.ee/doi/0A/0B/0A0B25526F599E87A1E8D7C612D23AF7205F0239978CBD9C491767A0C1D237CC.zip).
I fit the classifier following the exact commands in the tutorial (Fungal ITS analysis tutorial) and generated the classifier file: “unite-ver7-99-classifier-01.12.2017.qza”
The classification command I used was:
qiime feature-classifier classify-sklearn \
–i-classifier unite-ver7-99-classifier-01.12.2017.qza \
–i-reads seq.qza \
–p-confidence 0.7 \