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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy bugs >> crash after inferring trees with codon models http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1129114522 Message started by konrad on Oct 12^th, 2005 at 3:55am

Title: crash after inferring trees with codon models
Post by konrad on Oct 12^th, 2005 at 3:55am

Hi, I'm getting a crash on Windows XP, running HYPHY-P3.EXE (downloaded 11 Oct 2005), on the p51.nex example data set as follows:

1. load data set, select all, create partition.
2. set partition type codon, with universal code
3. set tree topology "infer tree"
4. set model GY94_3x4 (the crash occurs with all models I've tried), keep other settings at default
5. Likelihood->inference->infer toplogy; set to neighbour joining and use defaults for everything else

Now:
6. Likelihood->show parameters causes an immediate crash. Alternatively, fiddling around with the menus sometimes causes non-responsive behaviour and eventually a crash.

regards,
Konrad

Title: Re: crash after inferring trees with codon models
Post by Sergei on Oct 12^th, 2005 at 7:49am

Dear Konrad,

I am able to re-create the crash; thanks for the report.

After HyPhy infers a NJ tree (which takes no time at all), it then startes fitting the codon model you had selected to that tree (this takes a bit of time, maybe 10-15 seconds), after which the parameter table is opened automatically. If you wait for this, the program does not crash. However, if you open the parameter table while the likelihood function is still being optimized, a crash ensues (which is a bug).

I'll see what is causing the problem and post a fix. In the meantime, you can wait for the model fit to finish (there should be a progress indicator in the console status bar are while the optimization is taking place) before issuing new menu commands.

Cheers,
Sergei

Title: Re: crash after inferring trees with codon models
Post by konrad on Oct 12^th, 2005 at 8:50am

Thanks Sergei. The status bar was hidden beneath the windows taskbar at the bottom of my screen - you may want to look at the way the Hyphy console is resized and positioned on opening a data file.

Title: Re: crash after inferring trees with codon models
Post by Sergei on Oct 18^th, 2005 at 11:21am

Dear Konrad,

wrote on Oct 12^th, 2005 at 8:50am:

Thanks Sergei. The status bar was hidden beneath the windows taskbar at the bottom of my screen - you may want to look at the way the Hyphy console is resized and positioned on opening a data file.

I fixed this bug (as of today's build). I looked at the Win32 API documentation, and it wasn't immediately obvious to me how one can position windows (programmatically) whilst avoiding various taskbars. I'll look into that some more, as your observation of overlapping with the task bar is definitely in need of addressing.

Cheers,
Sergei