taxonomy assignment different result after re-training

#1

Hi,

Previously I had trained a custom plant ITS2 database (using qiime2 2019 04 fit naive bayes), and the taxonomy assignment looked pretty accurate at species level on the positive controls. However, yesterday I installed q2-clawback, but encountered some warnings about sckit learn version not compatible, and feature classifier external joblib deprecated, when I re-trained this database, and re-fit it to the reads, I got taxonomy assignment that was off the species level on those positive controls. I have removed qiime2 2019 04 and reinstalled it, and have not been able to reproduce the result again.

Not sure what is going on?

Thanks

#2

Which results can you not reproduce? Your original results, or, the “off the species level on those positive controls” results?

#3

The original results.

I am attaching the qzv files here, the provenace might help.

Orignal used the qiime2 2019 4 version when it was just released.
Yesterday used qiime2 2019 4 version from current.

I think most of the package versions are the same though.

Positive controls are CV (Cirsium vulgare), SO(Sidalcea oregana), VC (Vicia cracca) , and TM (Thermopsis montana)

original : original.qzv (757.5 KB)

yesterday: barplot_beepollen1.qzv (662.8 KB)

Thanks,

#4

Awesome, great idea!

You appear to have used two different reference databases between the two runs (according to the provenance capture):

Original

Reference taxonomy md5sum: 7a6a191f859d769b73b26f13cf39146f
Reference reads md5sum: 564023273711720746140ddf7ab04bdb

Redo

Reference taxonomy md5sum: dc6759734fe261d55389c949c24b2a09
Reference reads md5sum: f2d0863e291be7105f6d44dd6e0ab6fc

The original taxonomy is 8 levels deep, while the redo is only 7 levels deep.

Hope that helps!

#5

Thank you for the reply. They are actually the same in the content just the format, in the redo one, I removed the last ending colon from the original one ( before: …;s__xxx xxxx; now: …;s__xxx xxx). Would that effect the assignment?

#6

Hi @Xio_Lee — yes, removing one semicolon will remove an entire taxonomic level from the database.

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