EPA-NG taxa in tree not found in reference MSA

[Kenta Renard]

Hi,

I am confused as to why the error message "The reference Tree contained taxa that could not be found in the reference MSA" pops up when I try my EPA-NG run. The reference MSA I used is the same one that I used to generate the reference tree. I don't think it's an issue of reading the tree since it is saying the taxa in the tree can't be found in the MSA. Both MSAs are FASTA format and I checked that the taxa are there.

Could you please help me troubleshoot this?

Best wishes,
Kenta

[Alexandros Stamatakis]

Well maybe you did some post-processing or there is an issue with the
taxon names. Did you use RAxML to infer the tree or some other tool?

Are you getting a more concrete error message as to which taxon is missing?

It will be hard to help here without the actual data.

Alexis

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Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Kenta Renard]

Dear Alexandros,

Thank you for your reply. I used RAxML to infer the tree, yes. The error message says ALL the taxa found in the tree are not seen in the reference MSA. I have attatched both my query and reference MSAm, and the best model and tree file.

Best wishes,

Kenta

[Alexandros Stamatakis]

Dear Kenta,

I assume the problem is the discrepancy between FASTA and tree file
names, e.g. you have in fasta:

WP_006909616.1 hypothetical protein [Cyanobium sp. PCC 7001]

and in thy Newick file only:

((WP_006909616.1:

so I guess the part "hypothetical protein [Cyanobium sp. PCC 7001]" in
the fasta file is the problem and I would guess that if you remove all
that meta-information it should work,

Alexis

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>
> --
> Alexandros (Alexis) Stamatakis
>
> ERA Chair, Institute of Computer Science, Foundation for Research and
> Technology - Hellas
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>

> www.biocomp.gr <http://www.biocomp.gr> (Crete lab)
> www.exelixis-lab.org <http://www.exelixis-lab.org> (Heidelberg lab)

>
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