All features ids must be present in taxonomy, but the following feature ids are not:" and then many ID, like b47db366a25679dd507c550a23b82ace, 805a72c6085c867f05de73719aaf8870, 0367367b5700726abc795a11b382c763, b8ea2a4a5dae7de827152b8c21f643b1.
You need to use the taxonomy file that is created by running some form of feature classification. Otherwise, how can the table know anything about what taxon each feature is?
No, you don't need to necessary train a new classifier - proceed to qiime feature-classifier classify-sklearn, then use the output from that (FeatureData[Taxonomy]) as the taxonomy input to qiime taxa filter-table.
Edit: I forgot that your original issue was related to labels in the taxonomy --- yes, you will need to retrain, then reclassify, then you can filter.
I tried the potential solution (i.e., 1. qiime feature-classifier fit-classifier-naive-bayes; 2. qiime feature-classifier classify-sklearn; 3. qiime taxa filter-table) and the error is now at “qiime feature-classifier classify-sklearn.”
For qiime feature-classifier fit-classifier-naive-bayes [which worked], I did:
qiime feature-classifier fit-classifier-naive-bayes
–i-reference-reads silva-132-99-nb-otu.qza
–i-reference-taxonomy silva-132-99-taxonomy_NoSpaces.qza
–o-classifier silva-132-99-nb-classifier_NoSpaces.qza
For qiime feature-classifier classify-sklearn [which did not work], I did:
qiime feature-classifier classify-sklearn
–i-classifier silva-132-99-nb-classifier_NoSpaces.qza
–i-reads “Rep Seq file post pair, QC, and deblur”
–o-classification “Assign Taxa file post pair, QC, and deblur”
The error for the latter command was:
“Plugin error from feature-classifier:
pop from empty list”
Hi @Tyler_Carrier,
You must either not be using the SILVA 7-level taxonomy, or else you accidentally trimmed off some taxonomic data while removing terminal whitespace.
See here for a little more explanation of this error: