Plugin error from diversity - feature ids not corresponding to tip names

[Nicholas_Bokulich]

Hi @cjone228,

@cjone228

I know from other posts on the forum that this means there are features in my feature table not present on the tree, but I’m not sure how this could be possible since the tree and reference sequences I used to make my feature table were both from the gg-13-8 database.

Were the tree and reference sequences from identical OTU clustering thresholds? (this is how you can tell whether the tree was built from those reference sequences). I see that you are using the 97_otus phylogeny... but did you use the 97_otus rep_seqs as the reference for closed-reference OTU clustering?

It's probably not necessary yet (since I suspect this may just be an issue of pairing the wrong seqs/tree) but this post details a great way to open up and inspect your tree and table (using python — type "python" into your terminal and hit enter, hit "control + D" to exit when you are done):

feature ids much be present as tip names in phylogeny

Hey @laibinhuang! Let's take a closer look at the IDs in both of those Artifacts you have shared: import qiime2 import skbio import biom tree = qiime2.Artifact.load('EAA_AamoA_rootedtree.qza').view(skbio.TreeNode) table = qiime2.Artifact.load('EAA_AamoAtable.qza').view(biom.Table) tree_ids = {t.name for t in tree.tips()} table_ids = set(table.ids(axis='observation')) Then, if I print out the tree IDs: print(tree_ids) {'0048d0d890fb577f2bb2970047f0418734ac8df3 site4_AamoA_H03', '0291c9f44…