Re: [raxml] EPA-ng "Incompatible partition"

Alexandros Stamatakis

unread,

May 29, 2024, 3:57:35 AMMay 29

to ra...@googlegroups.com

Dear Kenta,

I could imagine that the taxon names like:

>New|New|NEW_WP_300875191.1/1-360 photosystem II q(b) protein
[Thermosynechococcus sp. Uc]

might be causing the issue, maybe replacing them by simpler ones:

e.g., NEW_WP_300875191 might solve the issue?

Otherwise, let me know and I will have a closer look.

Alexis

On 28.05.24 21:11, Kenta Renard wrote:
> Dear All,
>
> I am trying to place 8 tips into a reference tree but I have been
> spending hours trying to get it to work but it keeps spitting out the
> "incompatible partition" error message and I am not sure what is causing
> it. I have checked the query and input and I cannot figure out what is
> wrong. I have attached all of the files below.
>
> test.txt is the query and the fasta file is the reference. g.tre is the
> tree file.
>
> Best,
> Kenta
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/raxml/0a8fef99-47c4-4531-99ae-198182dcf3d2n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/0a8fef99-47c4-4531-99ae-198182dcf3d2n%40googlegroups.com?utm_medium=email&utm_source=footer>.

--
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

unread,

May 29, 2024, 7:13:44 AMMay 29

to raxml

Dear Alexis,

Thank you for the reply. No matter what I change the names of the query taxa to, the issue persists. If it is worth noting, I aligned the queries to the reference fasta using MAFFT. I am quite confused as I used this method before and EPA-ng worked fine. Could you please have a closer look? Meanwhile I will try and aligning the queries using PaPaRa and see if anything changes.

Best wishes,

Kenta

Kenta Renard

unread,

May 29, 2024, 8:09:09 AMMay 29

to raxml

Dear Alexis,

It is still not working when I aligned the queries with PaPaRa (and used the EPA-ng --split function). I have attached the output error message from the terminal if this helps.

Best,

Kenta

On Wednesday 29 May 2024 at 08:57:35 UTC+1 Alexandros Stamatakis wrote:

epa-ng_error.png

Alexandros Stamatakis

unread,

May 29, 2024, 11:34:38 AMMay 29

to ra...@googlegroups.com

can you send me the command line you used?

Alexis

> https://groups.google.com/d/msgid/raxml/0a8fef99-47c4-4531-99ae-198182dcf3d2n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/0a8fef99-47c4-4531-99ae-198182dcf3d2n%40googlegroups.com> <https://groups.google.com/d/msgid/raxml/0a8fef99-47c4-4531-99ae-198182dcf3d2n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/0a8fef99-47c4-4531-99ae-198182dcf3d2n%40googlegroups.com?utm_medium=email&utm_source=footer>>.

>
> --
> 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)

>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/raxml/5c79a509-d5ee-4ab4-87dd-40715dd01f77n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/5c79a509-d5ee-4ab4-87dd-40715dd01f77n%40googlegroups.com?utm_medium=email&utm_source=footer>.

Kenta Renard

unread,

May 29, 2024, 11:48:45 AMMay 29

to raxml

Dear Alexis,

Here it is:

./epa-ng --tree g.tre -s reference_g3bless_edited.fasta --query test.txt --model G3_D1int_evaluate_.raxml.bestModel --redo

I have attatched the .bestModel file if needed too.

Best wishes,

Kenta

G3_D1int_evaluate_.raxml.bestModel

Alexandros Stamatakis

unread,

May 29, 2024, 12:14:32 PMMay 29

to ra...@googlegroups.com

Okay and now I would need the command line you used to produce the:

G3_D1int_evaluate_.raxml.bestModel

file, and the file itself as well please.

Alexis

> >
> > --
> > 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> <http://www.biocomp.gr

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

> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>

> (Heidelberg lab)
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send
> > an email to raxml+un...@googlegroups.com
> > <mailto:raxml+un...@googlegroups.com>.
> > To view this discussion on the web visit
> >

> https://groups.google.com/d/msgid/raxml/5c79a509-d5ee-4ab4-87dd-40715dd01f77n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/5c79a509-d5ee-4ab4-87dd-40715dd01f77n%40googlegroups.com> <https://groups.google.com/d/msgid/raxml/5c79a509-d5ee-4ab4-87dd-40715dd01f77n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/5c79a509-d5ee-4ab4-87dd-40715dd01f77n%40googlegroups.com?utm_medium=email&utm_source=footer>>.

>
> --
> 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)
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/raxml/60c685a2-ce08-45e1-9ec0-8b54387fa683n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/60c685a2-ce08-45e1-9ec0-8b54387fa683n%40googlegroups.com?utm_medium=email&utm_source=footer>.

Kenta Renard

unread,

May 29, 2024, 12:25:27 PMMay 29

to raxml

The command line for that was:

./raxml-ng --evaluate --msa input_msa.fasta --tree G3_D1int_ML.raxml.bestTree --prefix G3_D1int_evaluate_ --model LG4M+IO --opt-branches on --opt-model on --redo

I attatched the file in the previous message but I will do again here. I tried not using that bestModel file but even if I use others or even just specify "LG4M+IO", the issue remains.

Best,

Kenta

G3_D1int_evaluate_.raxml.bestModel

Kenta Renard

unread,

May 30, 2024, 8:58:09 AMMay 30

to raxml

Dear Alexis,

When I specified a different evolutionary model in EPA-ng compared to the one I used to build the tree in RAxML-ng (which was LG4M) then the tips were able to be placed. In this situation, what should I do? I want the tips to be placed as accurately as possible but I can't place the tips unless I change the evolutionary model. Is this bug able to be fixed?

Best,

Kenta

On Wednesday 29 May 2024 at 17:14:32 UTC+1 Alexandros Stamatakis wrote:

Alexandros Stamatakis

unread,

May 30, 2024, 9:55:18 AMMay 30

to ra...@googlegroups.com

Dear Kenta,

Well I would say that it shouldn't matter that much for the placement, I
assume that what you are observing is just an inconsistency between the
models available in RAxML-NG and EPA-NG.

I will check what is happening, but please give me some time as this
period is very busy.

Cheers,

Alexis

> > >
> > > --
> > > 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> <http://www.biocomp.gr

> <http://www.biocomp.gr>> <http://www.biocomp.gr <http://www.biocomp.gr>

> > <http://www.biocomp.gr <http://www.biocomp.gr>>> (Crete lab)
> > > www.exelixis-lab.org <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>
> > <http://www.exelixis-lab.org <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>>
> > (Heidelberg lab)
> > >
> > > --
> > > You received this message because you are subscribed to the Google
> > > Groups "raxml" group.
> > > To unsubscribe from this group and stop receiving emails from it,
> > send
> > > an email to raxml+un...@googlegroups.com
> > > <mailto:raxml+un...@googlegroups.com>.
> > > To view this discussion on the web visit
> > >
> >

> >
> > --
> > 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> <http://www.biocomp.gr
> <http://www.biocomp.gr>> (Crete lab)
> > www.exelixis-lab.org <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>
> (Heidelberg lab)
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send
> > an email to raxml+un...@googlegroups.com
> > <mailto:raxml+un...@googlegroups.com>.
> > To view this discussion on the web visit
> >

> https://groups.google.com/d/msgid/raxml/60c685a2-ce08-45e1-9ec0-8b54387fa683n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/60c685a2-ce08-45e1-9ec0-8b54387fa683n%40googlegroups.com> <https://groups.google.com/d/msgid/raxml/60c685a2-ce08-45e1-9ec0-8b54387fa683n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/60c685a2-ce08-45e1-9ec0-8b54387fa683n%40googlegroups.com?utm_medium=email&utm_source=footer>>.

>
> --
> 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)
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/raxml/b88022f0-2f34-45ca-88eb-235f6a01d37bn%40googlegroups.com <https://groups.google.com/d/msgid/raxml/b88022f0-2f34-45ca-88eb-235f6a01d37bn%40googlegroups.com?utm_medium=email&utm_source=footer>.

Lucas Czech

unread,

May 31, 2024, 2:18:35 AMMay 31

to ra...@googlegroups.com

Hi Kenta,

can you please share the first few lines of each file that you are using? For instance, you can use the `head` command to get those. Furthermore, can you please share the exact command that you used to run EPA-ng?

Cheers and thanks
Lucas

Dr. Lucas Czech

Postdoctoral Fellow

University of Copenhagen

Faculty of Health and Medical Sciences

Globe Institute, Section for GeoGenetics

lucas...@sund.ku.dk

Logo for Københavns Universitet

Alexandros Stamatakis

unread,

May 31, 2024, 2:27:00 AMMay 31

to ra...@googlegroups.com

Lucas, I already have them will fwd them to you,

Alexis

>> https://groups.google.com/d/msgid/raxml/0a8fef99-47c4-4531-99ae-198182dcf3d2n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/0a8fef99-47c4-4531-99ae-198182dcf3d2n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/0a8fef99-47c4-4531-99ae-198182dcf3d2n%40googlegroups.com?utm_medium=email&utm_source=footer>>.

>>
>> --
>> 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)
>>

> *Dr. Lucas Czech *
>
> Postdoctoral Fellow
>
> *University of Copenhagen *

>
> Faculty of Health and Medical Sciences
>
> Globe Institute, Section for GeoGenetics
>

> _lucas...@sund.ku.dk_ <mailto:lucas...@sund.ku.dk>
>
> Logo for Københavns Universitet

>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/raxml/b2ac4baa-53da-4007-8c2a-9791f540b87f%40gmail.com <https://groups.google.com/d/msgid/raxml/b2ac4baa-53da-4007-8c2a-9791f540b87f%40gmail.com?utm_medium=email&utm_source=footer>.

Reply all

Reply to author

Forward