Core-metrics-phylogenetic Error: the table does not appear to be completely represented by the phylogeny.

[TurboQiimer]

Hi all,

I just got this error. I found this thread to solve the error but not worked.

qiime diversity core-metrics-phylogenetic \

--i-phylogeny rooted-tree-DNA-36-DNA.qza
--i-table 3-Merged-Tables-mcrA-DNA-Ungrouped.qza
--p-sampling-depth 1310
--m-metadata-file Merged-Metadata-mcrA-DNA.tsv
--output-dir core-metrics-results-36-mcrA-DNA

Plugin error from diversity:

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

Debug info has been saved to /tmp/qiime2-q2cli-err-m_bmnyul.log

I filtered rep-seq by this command:

qiime feature-table filter-seqs
--i-data 3-Merged-Rep.Seq-mcrA-DNA-Ungrouped.qza
--i-table 3-Merged-Tables-mcrA-DNA-Ungrouped.qza
--o-filtered-data 3-Merged-Rep.Seq-mcrA-DNA-Ungrouped-filtered.qza

I do not know the error origin! I need your help.

Also, it is my frequency per sample table!

Thanks a lot
Qiimer

[TurboQiimer]

I used Qiime2 version 2020.08.

[Nicholas_Bokulich]

Hi @TurboQiimer,
As the error indicates, your phylogeny is missing sequence IDs that are found in the table.

Most likely, you made a tree from the wrong sequences, or not all of the sequences.

@TurboQiimer

3-Merged-Tables-mcrA-DNA-Ungrouped.qza

sounds like you merged multiple tables. Make sure that you merge the associated sequences from each, and then build a tree from the merged sequences.

@TurboQiimer

I found this thread to solve the error but not worked.

This is a common issue and there are many other related topics out there — I recommend digging more into the archives for more related scenarios/troubleshooting advice.

Good luck!