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

[cjone228 (Carli Jones)]

Hi all,

I did closed reference OTU clustering with my data and I am now trying to do core metrics analysis. I got the following error:

Plugin error from diversity:

**All ``feature_ids`` must be present as tip names in ``phylogeny``. ``feature_ids`` not corresponding to tip names (n=18947): 712377142190547bd0d6f53bfaccd504 f1812e3a61f77e219ce73fadaa06abc1...........**

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. Below is my code for the core metrics analysis that failed:

qiime diversity core-metrics-phylogenetic \
  --i-table ~/scratch/Carli/feature_table_5-6-20.qza  \
  --i-phylogeny ~/work/gg-13-8/trees/97_otus.qza \
  --m-metadata-file ~/scratch/Carli/ORIOLE_metadata-5-6-20.tsv \
  --p-sampling-depth 80000 \
  --output-dir ~/scratch/Carli/core_metrics_results_5-7-20 \
  --verbose

Does anyone have any suggestions? Thank you!
Carli

[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…

[jwdebelius (Justine Debelius)]

Hi @cjone228,

The tip names you have don’t look like tip names for Greengenes. Those are ASV names, and greengenes typically has numbered indentifiers. Is there any chance you passed an ASV table instead of your OTU table?

Best,
Justine

[cjone228 (Carli Jones)]

@Nicholas_Bokulich and @jwdebelius, thank you!!! My brain is turning to mush and it took making this post to see that I used my original feature table instead of the closed reference OTU table… oops