# Error message: The table does not appear to be completely represented by the phylogeny.
**URL:** https://forum.qiime2.org/t/error-message-the-table-does-not-appear-to-be-completely-represented-by-the-phylogeny/21049
**Category:** Technical Support
**Created:** [October 12, 2021, 7:49pm UTC](https://forum.qiime2.org/t/error-message-the-table-does-not-appear-to-be-completely-represented-by-the-phylogeny/21049 "2021-10-12T19:49:49Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@AHK](https://forum.qiime2.org/u/AHK)
#### Post date: [October 12, 2021, 7:49pm UTC](https://forum.qiime2.org/t/error-message-the-table-does-not-appear-to-be-completely-represented-by-the-phylogeny/21049/1 "2021-10-12T19:49:49Z")
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](https://forum.qiime2.org/uploads/short-url/gnQNtN0yrWKML8n1e3g1HRRag1F.qza) (2.5 MB) [dada2\_table6.qza](https://forum.qiime2.org/uploads/short-url/zhYENnjBJPmhp41DaFrv3F1uEYK.qza) (873.1 KB).
I appreciate your help!
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---
### Author:  [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [October 13, 2021, 2:35pm UTC](https://forum.qiime2.org/t/error-message-the-table-does-not-appear-to-be-completely-represented-by-the-phylogeny/21049/2 "2021-10-13T14:35:50Z")
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](https://library.qiime2.org/plugins/q2-fragment-insertion/16/) you need to run the following command to filter your table:
```auto
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:
```auto
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
```
---
### Author:  [@AHK](https://forum.qiime2.org/u/AHK)
#### Post date: [October 14, 2021, 3:04pm UTC](https://forum.qiime2.org/t/error-message-the-table-does-not-appear-to-be-completely-represented-by-the-phylogeny/21049/3 "2021-10-14T15:04:20Z")
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!
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [November 14, 2021, 9:04pm UTC](https://forum.qiime2.org/t/error-message-the-table-does-not-appear-to-be-completely-represented-by-the-phylogeny/21049/4 "2021-11-14T21:04:42Z")
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