Plugin error from diversity: The table does not appear to be completely represented by the phylogeny.

Hi qiime team,

As I'm trying to calculating unifrac distance between patients diet data, I have met this problem:
Plugin error from diversity: The table does not appear to be completely represented by the phylogeny.

The feature table(with correct feature name and fake data) and the tree are attached

food_cts_fake.qza (527.0 KB)

output_food_tree_datatree.qza (14.3 KB)

The complete error message is below
`Traceback (most recent call last):
File "//anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "<//anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-373>", line 2, in beta_phylogenetic
File "//anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "//anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in callable_executor
output_views = self._callable(**view_args)
File "//anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_diversity/_beta/_method.py", line 86, in beta_phylogenetic
variance_adjusted=variance_adjusted, bypass_tips=bypass_tips)
File "//anaconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/unifrac/_methods.py", line 103, in unweighted
variance_adjusted, 1.0, bypass_tips, threads)
File "unifrac/_api.pyx", line 86, in unifrac._api.ssu
ValueError: The table does not appear to be completely represented by the phylogeny.

Plugin error from diversity:

The table does not appear to be completely represented by the phylogeny.

See above for debug info.`

Can anybody help identify how to resolve this issue?

Angel

The beta diversity command I ran:

qiime diversity beta-phylogenetic \

–i-table food_cts_fake.qza
–i-phylogeny …/source/output_food_tree_datatree.qza
–p-metric unweighted_unifrac
–o-distance-matrix unweighted_unifrac_distance_matrix.qza

Hi @adai

I think i might have an idea of why your command isn’t working. I looked at the tree.nwk file inside of your tree and it has underscores in the features (i.e. Apple_juice__100) while your feature table has spaces (i.e. Apple juice 100). Can you try creating a new feature table from food_cts_fake.qza that replaces the spaces with underscores and run the diversity command again?

4 Likes

Hi Gibs,

Thank you for the reply.

I deliberately replaced the underscore with the spaces, since when I’m calculating alpha diversity with a tree, I found the tips of the tree are stored in the python script in the format with only spaces. So in order to align the feature table and the tree, I make sure the feature names are with spaces only. I talked about it in an earlier post from me: All ``feature_ids`` must be present as tip names in ``phylogeny``. Tips missing when converting the newick tree to qza format

With the fake data I posted here, you have no problem calculating the alpha diversity with Faith distance.

But I ran into problems when calculating the unifrac diversity, and I haven’t seen this error message in the forum before

Angel

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