Re: [raxml] Errors when optimizing model parameters+branch lengths for a given input tree

[Alexandros Stamatakis]

are you sure that you called raxml the second time with the correct tree
file name? Both trees are called: Topology_I.tree

please double check this and if the problem persists please send me the
alignment file to my personal email such that I can check.

Alternatively you might want to consider using raxml-ng fron now on:

https://github.com/amkozlov/raxml-ng

alexis

On 13.01.2018 11:38, sean...@tmu.edu.tw wrote:
> Hi
>
> I am running RaxML and have the following errors. Hope someone can help me!
>
> 1. I have a tree like this:
>
> ((Turt,(Ixod,Smim)),(Stri,(((Hazt,(Eaff,(Tcal,Lsal))),((Dpul,Dmag),(CAQU,(Cspl,(Znev,((Apis,Clec),(Amel,(Tcas,(Dmel,Hmel))))))))))));
>
>
> RAxML was called as follows:
>
> raxmlHPC-PTHREADS -T 30 -f e -m PROTGAMMALGF -s 778.phylip -t
> Topology_I.tree -n Topology_I
>
> ERROR: Too many internal nodes.  Is tree rooted?
>
>        Deepest splitting should be a trifurcation.
>
> raxmlHPC-PTHREADS: treeIO.c:1413: treeReadLen: Assertion `0' failed.
>
> Aborted (core dumped)
>
> 2. I then I then make the tree trifurcated.
>
> (Turt,(Ixod,Smim),(Stri,(((Hazt,(Eaff,(Tcal,Lsal))),((Dpul,Dmag),(CAQU,(Cspl,(Znev,((Apis,Clec),(Amel,(Tcas,(Dmel,Hmel))))))))))));
>
>
> RAxML was called as follows:
>
> raxmlHPC-PTHREADS -T 30 -f e -m PROTGAMMALGF -s 778.phylip -t
> Topology_I_1.tree -n Topology_I_1
>
> ERROR: Expecting ',' in tree; found: character ')'
>
> ,(Dmel,Hmel))))))))))));
>                     ^
> RAxML may be expecting to read a tree that contains branch lengths
>
> raxmlHPC-PTHREADS: treeIO.c:1419: treeReadLen: Assertion `0' failed.
>
> Aborted (core dumped)
>
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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org