Using a Classifier, Error: Classifier does not support confidence values

[aalex (Andrea)]

I reran the command after adding the spaces between the semi-colons (I thought just to try it)

qiime feature-classifier classify-consensus-vsearch
--i-query Qiime_try/rep-seqs.qza
--i-reference-reads arthropoda_sequence-BOLD.qza
--i-reference-taxonomy arthropoda_taxonomy-BOLD.qza
--p-threads 3
--o-classification vsearch-consensus-classification.qza
--verbose

And it seems to have rectified what issues I had before.

The output for

cat taxonomy.tsv | grep ‘s__.’ | head

is now

d9a139aad43b47127cdf950895e6c2e9 k__Animalia; p__Arthropoda; c__Insecta; o__Trichoptera; f__Phryganeidae; g__Agrypnia; s__Agrypnia improba

(there's more it's just a bit clunky)

And the taxonomy collapse works to the species level

I attached the most recent vsearch output to the google drive nonetheless.

[Nicholas_Bokulich]

@aalex

I reran the command after adding the spaces between the semi-colons (I thought just to try it)

I'm glad you tried but I am astounded; the spaces should not be necessary at all. I wonder if the original file had invisible characters that caused your issue?

In any case, now it sounds like everything is not only working but working extremely well (if that species-level classification is characteristic of your results at large). So maybe let's just file this in the "unsolved mysteries" drawer and move on!

[aalex (Andrea)]

Haha sounds good! Thank you again, both, for all your help!