I’ve looked more into this issue. And I’ve found the ultimate problem
In my newick tree, the tips are like this: “Cauliflower__cooked__from_fresh__made”
but when its read into the program and the function _validate_otu_ids_and_tree extracts the tips in the format of absolutely no underscores. All of the underscores have been replaced with spaces.
That is why it doesn’t match with my features in the feature table, since I have underscores.
I think to get it to work, I can just have features having no underscores as well.
But if anybody is interested in clearing the confusion. Welcome!
Otherwise, this issue could be considered resolved.
Angel