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

[AHK]

Hi,
I am getting the following error message ' Plugin error from diversity: The table does not appear to be completely represented by the phylogeny.'.

In the form, I found a similar error message; I tried to troubleshoot the problem based on the recommendations on other posts. Still, I am having difficulty solving the issue I have.

Based on the feature table, I chose the sampling depth of 23483 when executing qiime diversity core-metrics-phylogenetic. I believe I have enough features (65.92%) in (88.24%) samples at 23483 sampling depth.

The command I ran to generate the tree is below:
qiime fragment-insertion sepp
--i-representative-sequences ./dada2_rep_set.qza
--i-reference-database sepp-refs-gg-13-8.qza
--o-tree ./tree2.qza
--o-placements ./tree_placements.qza
--p-threads 12

The command I ran for diversity analysis is below:
qiime diversity core-metrics-phylogenetic
--i-table ./dada2_table6.qza
--i-phylogeny ./tree.qza
--m-metadata-file ./metadata.tsv
--p-sampling-depth 23483
--output-dir ./core-metrics-results

To note, the error message begins at 599 sampling depth.

Attached are the qza files for the table and the tree:
tree2.qza (2.5 MB) dada2_table6.qza (873.1 KB).

I appreciate your help!

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[SoilRotifer (Mike Robeson)]

Hi @AHK,

The feature table needs to be filtered based on the tree2.qza output from fragment-insertion. I'm not sure where tree.qza comes from... in your core-metrics-phylogneetic command. Typo?

As per the fragment-insertion tutorial you need to run the following command to filter your table:

qiime fragment-insertion filter-features \
    --i-table ./dada2_table6.qza \
    --i-tree ./tree2.qza \
    --o-filtered-table ./dada2_table6_filt.qza \
    --o-removed-table ./dada2_table6_removed.qza

Then you should be able to run core-metrics-phylogenetic like so:

qiime diversity core-metrics-phylogenetic \
    --i-table ./dada2_table6_filt.qza \
    --i-phylogeny ./tree2.qza \
    --m-metadata-file ./metadata.tsv \
    --p-sampling-depth 23483 \
    --output-dir ./core-metrics-results 

[AHK]

Thank you Mike!
The tree.qza in core-metrics-phylogenetic command came from the output of fragment-insertion sepp command. Under Qiime2 Doc tutorials, I do not see a statement that says it is necessary to filter out the feature table. Now that you brought it to my attention, it makes sense. I ran the command to filter the table, then re-ran the core-metrics-phylogenetic command, and it's working. I appreciate your help!