exabayes consense issue

[Shoyo Sato]

Hello,

I think I am getting the same error as Dr. Faircloth (https://groups.google.com/u/1/g/exabayes/c/7n5kxaLRNWc/m/d-yYOSY3uB0J) but with version 1.5.1. I tried adding additional iterations as Dr. Faircloth suggested and still could not create a consensus. Maybe I got unlucky and hit these rare cases multiple times.

Here is the error:

consense: ./src/contrib/ConsensusTree.cpp:111: std::__cxx11::string ConsensusTree::getConsensusTreeString(bool) const: Assertion `consensus.size() <= maxBip' failed.

I'd be more than happy to send over data and topology files if needed!

Thank you so much for your help!

Best,

Shoyo

[Alexandros Stamatakis]

Dear Shoyo,

Have you seen the related discussion on the raxml google group?

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)

[Shoyo Sato]

Hi Alexis,

Thank you for your response. I completely forgot about this utility!

Sorry if I am missing something but when I consense with raxml, I lose the branch length information. Is there a way to retain this as with exabayes?

Best,

Shoyo

[Alexandros Stamatakis]

Dear Shoyo,

I am afraid not, but I am ccing Alexey who has developed RAxML-NG.

Alexey, given the recurrent consensus problems with ExaBayes that have
been reported to us it might be worthwhile implementing this in the
RAxML-NG consensus function?

Alexis

On 11.01.24 14:10, Shoyo Sato wrote:
> Hi Alexis,
>
> Thank you for your response. I completely forgot about this utility!
> Sorry if I am missing something but when I consense with raxml, I lose
> the branch length information. Is there a way to retain this as with
> exabayes?
>
> Best,
> Shoyo
>
> On Wednesday, January 10, 2024 at 12:02:16 PM UTC+1
> alexandros...@gmail.com wrote:
>
> Dear Shoyo,
>
> Have you seen the related discussion on the raxml google group?
>
> Alexis
>
> On 09.01.24 13:53, Shoyo Sato wrote:
> > Hello,
> >
> > I think I am getting the same error as Dr. Faircloth
> >

> (https://groups.google.com/u/1/g/exabayes/c/7n5kxaLRNWc/m/d-yYOSY3uB0J <https://groups.google.com/u/1/g/exabayes/c/7n5kxaLRNWc/m/d-yYOSY3uB0J>)

> > but with version 1.5.1. I tried adding additional iterations as Dr.
> > Faircloth suggested and still could not create a consensus. Maybe
> I got
> > unlucky and hit these rare cases multiple times.
> >
> > Here is the error:
> >
> > consense: ./src/contrib/ConsensusTree.cpp:111: std::__cxx11::string
> > ConsensusTree::getConsensusTreeString(bool) const: Assertion
> > `consensus.size() <= maxBip' failed.
> >
> > I'd be more than happy to send over data and topology files if
> needed!
> >
> > Thank you so much for your help!
> >
> > Best,
> >
> > Shoyo
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "ExaBayes" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send
> > an email to exabayes+u...@googlegroups.com
> > <mailto:exabayes+u...@googlegroups.com>.
> > To view this discussion on the web visit
> >

> https://groups.google.com/d/msgid/exabayes/a8b4e66f-141e-4294-9508-81d64506812bn%40googlegroups.com <https://groups.google.com/d/msgid/exabayes/a8b4e66f-141e-4294-9508-81d64506812bn%40googlegroups.com> <https://groups.google.com/d/msgid/exabayes/a8b4e66f-141e-4294-9508-81d64506812bn%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/exabayes/a8b4e66f-141e-4294-9508-81d64506812bn%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)

>
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> https://groups.google.com/d/msgid/exabayes/b8652a75-981d-4293-925a-80075a69c169n%40googlegroups.com <https://groups.google.com/d/msgid/exabayes/b8652a75-981d-4293-925a-80075a69c169n%40googlegroups.com?utm_medium=email&utm_source=footer>.