Plugin error from feature-classifier: pop from empty list (but the taxonomy is not incomplete)

[Nicholas_Bokulich]

Hi @ncep112 ,
Thanks for reporting your issue here.

This can be caused by even a single missing taxonomy. Could you please share the output of tabulate?

See also this topic — if you selected more than the standard 7 ranks then dereplicate lca mode will not work:

qiime rescript dereplicate --p-mode super leads to "Taxonomic label depth is uneven" error with qiime rescript evaluate-fit-classifier

HI @David_Bradshaw, The dereplicate action was initially set up to handle taxonomies with only the standard 7-ranks (i.e. dpcofgs). That is, if any taxonomy was truncated at a higher level, we'd backfill them with the corresponding prefixes, e.g. f__; g__; s__. For example, this: KJ763795.1.1805 d__Eukaryota; k__Alveolata; p__Dinoflagellata; c__Dinophyceae; o__Gymnodiniphycidae would become this: KJ763795.1.1805 d__Eukaryota; k__Alveolata; p__Dinoflagellata; c__Dinophyceae; o__Gymnodiniphyc…

If you can find the taxonomy that is missing a rank (or even the entire annotation), you can use the replace-taxonomy action in RESCRIPt to edit the taxonomy.

As you are using the classify-sklearn classifier, I would recommend dereplicating with uniq mode, as the Naive Bayes classifier is essentially finding the LCA anyway.

@ncep112

silva-138-ssu-nr99-515f-806r-classifier.qza

Are you aware of the pre-trained classifiers available on the QIIME 2 data resources page?

Data resources — QIIME 2 2022.2.0 documentation

There are pre-trained SILVA classifiers available there, trimmed to the 515f-806r region; but I am guessing that you want some customization (e.g., non-standard ranks), just want to make sure.