Assigning taxonomy and filtering chloroplasts/mitochondria- removing all sample IDs?

[Nicholas_Bokulich]

@ncep112

And I couldn’t check for every single ID that was listed, but I didn’t see any errors (all of the IDs that I checked were present in both files without any repeats). And I searched for some of the IDs listed in the error message, and they were present in my table.qzv and rep-seqs.qzv files as well.

Really? I just checked and none of the feature IDs match. I checked both manually and with the following python code (which confirms that no feature IDs are shared)

>>> import biom
>>> import qiime2
>>> import pandas as pd
>>> tab = qiime2.Artifact.load('table.qza')
>>> tax = qiime2.Artifact.load('taxonomy-without-spaces_LP.qza')
>>> tab_ids = tab.view(biom.Table).ids('observation')
>>> tax_ids = tax.view(pd.Series).index
>>> set(tab_ids) & set(tax_ids)
set()

Unfortunately, I cannot check the provenance since you exported the data, but looking at the commands you shared above it is not clear where taxonomy-without-spaces_LP.qza came from. I recommend re-checking those commands carefully to make sure you are using the correct files.

Good luck!