error when running raxmlHPC-PTHREADS-SSE3 with RNA secondary structure

[Paul Simion]

Hello,

I am running analyses with/without RNA secondary structure information, and the the analysis aborts after the first ML search when I use secondary structure.
The first analysis worked well with the following command :
raxmlHPC-PTHREADS-SSE3 -T 6 -p 12345 -f d -# 100 -s 18S_CNIDO_GB_rdy.phy -m GTRGAMMAI -n 18S_CNIDO

The second fails after the first tree is computed, using this command :
raxmlHPC-PTHREADS-SSE3 -T 6 -p 12345 -f d -# 100 -s 18S_CNIDO_GB_rdy.phy -S STRUCTURE_18S_ALL_GB.txt -m GTRGAMMAI -A S16 -n 18S_CNIDO_STRUCTURE

the output and the aborting message is as follows :
_________________________________________________
Partition: 0 with name: No Name Provided
Base frequencies: 0.350 0.168 0.222 0.261

Partition: 1 with name: SECONDARY STRUCTURE 16 STATE MODEL
Base frequencies: 0.013 0.012 0.010 0.152 0.013 0.016 0.179 0.015 0.021 0.206 0.025 0.067 0.158 0.013 0.061 0.038

-9727.196136 -9724.849809
raxmlHPC-PTHREADS-SSE3: optimizeModel.c:3806: modOpt: Assertion `tr->likelihood >= currentLikelihood' failed.
zsh: abort      ./raxmlHPC-PTHREADS-SSE3 -T 6 -p 12345 -f d -# 100 -s 18S_CNIDO_GB_rdy.phy -S
_________________________________________________

Does anyone have any ideas of what could cause this ?
Thank you anyway !

Paul Simion

PS : I know I shouldn't use the estimation of the proportion of invariant site :)

[Alexandros Stamatakis]

Dear Paul,

Could you please send me the input data files to my private email
address?

Thanks,

Alexis

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Alexandros Stamatakis]

Hi Paul,

I am looking at the bug right now. It seems to be associated with the
branch length optimization under +I.

In the meantime you can use -m GTRGAMMA that one should work.

Alexis

On Fri, 2013-05-17 at 04:50 -0700, Paul Simion wrote:

[Alexandros Stamatakis]

the bug is fixed, I just pushed a new version to github,
the bug only appeared for +I in combination with secondary structure
models

Alexis

On Fri, 2013-05-17 at 04:50 -0700, Paul Simion wrote:

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