pre-trained UNITE ITS classifiers for QIIME 2024.10 (and older!)

[colinbrislawn (Colin J Brislawn)]

UNITE version 10.0 was updated on 2025-02-19, and I've built classifiers for it compatible with the newest version of Qiime2:

Releases · colinbrislawn/unite-train

Other notes

Eventually, this will be superseded when UNITE is provided directly on the Data Resources Page.

Not what you are looking for? Please send me a direct message or open an issue.

Colin

[Zango (Sauban Musa Jibril)]

Thank you very much Sir

[Sam_Degregori]

I see "all" eukaryotes? Does this mean CO1?

[colinbrislawn (Colin J Brislawn)]

Good question! I think UNITE is ITS only (so, no CO1 to my knowledge)

You can read more on their page: UNITE - Resources

[Taylor_Akers]

Hello @colinbrislawn - I have a novice question about using this pre-trained classifier.

The qza files available in the GitHub link you posted, can these be used directly in the "test the classifier" portion of this q2-feature-classifier tutorial?

Ex:
qiime feature-classifier classify-sklearn
--i-classifier unite_ver9_dynamic_25.07.2023-Q2-2023.9.qza
--i-reads rep-seqs.qza
--o-classification taxonomy.qza

[cherman2 (Chloe Herman)]

Hi @Taylor_Akers,
From what I understand, this should work!

[Taylor_Akers]

Great, thank you @cherman2 ! It worked!

[emmlemore]

Hi @colinbrislawn thank you for creating this classifier!

I downloaded the latest version and tried it with my data. However, it runs for about 20 minutes before the job is killed. I am assuming this is due to insufficient RAM (I have 16GB)?

In that case, I should likely create my own classifier using RESCRIPt? Thank you.

[colinbrislawn (Colin J Brislawn)]

@emmlemore

I am assuming this is due to insufficient RAM (I have 16GB)?

In that case, I should likely create my own classifier using RESCRIPt? Thank you.

Making a new classifier takes more memory then using an existing classifier. Using one of these pre-made ones still probably your best option with limited memory...

I would try using a smaller number of reads per batch, say
--p-reads-per-batch 5000 or 1000.

Also consider using a search-based classifier like
qiime feature-classifier classify-consensus-blast

[Steven_Criollo]

I have the same issue—after updating QIIME2 to version 2025.4, the classifiers no longer work. When I try to use them, the execution gets interrupted. I don’t think it’s a RAM issue since I have 16GB, and I had no problems with the previous classifiers and QIIME2 version 2023.9. What could be the cause?

[gregcaporaso]

Hi @Steven_Criollo, Are you using newly trained classifiers, or classifiers that were trained for QIIME 2 2023.9? The classifiers need to be updated every time we update to a new version of scikit-learn, and we did that in 2024.10, so pre-2024.10 classifiers won't work with 2025.4. @colinbrislawn has new ones trained which you can download from his git repository.