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HYPHY Package >> HyPhy bugs >> Open a tree file... crashes Hyphy
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1374191104

Message started by lu on Jul 18th, 2013 at 4:45pm

Title: Open a tree file... crashes Hyphy
Post by lu on Jul 18th, 2013 at 4:45pm
Hi,
I use Hyphy for MacOS and as soon as I want to load a tree file, the program closes immediately.
There is no error message.
I tried this with many different tree files, generated with different methods and with different file types, but the problem is always present.
Do you know how to deal with this?
Thank you very much for your help!
Lu

Title: Re: Open a tree file... crashes Hyphy
Post by lu on Jul 18th, 2013 at 4:59pm
I am using HYPHY 2.220130702beta(MP) for MasOS
lu

Title: Re: Open a tree file... crashes Hyphy
Post by Steven on Jul 18th, 2013 at 5:35pm
Hi Lu,

Good to see that you've made it onto the forums.

May I inquire which version of OSX you have?

I'm running OSX 10.8.4 and running the attached file without issue.
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=test_newick.txt (0 KB | 2 )

Title: Re: Open a tree file... crashes Hyphy
Post by lu on Jul 19th, 2013 at 11:56am
Thanks for the follow-up.
I am using Mas OS X 10.7.5.
I am also running without problem the file you sent me though I cannot run other files I have.
For example see attached file.
Thank you for your help.
Lu
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=test-tree3.txt (0 KB | 2 )

Title: Re: Open a tree file... crashes Hyphy
Post by Steven on Jul 19th, 2013 at 12:13pm
Until we can fix this problem, you may want to try using HyPhy 2.1 found here:

Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login

or update OSX to the latest version.

Best,
Steven

Title: Re: Open a tree file... crashes Hyphy
Post by Sergei on Jul 23rd, 2013 at 4:02pm
Hi Lu,

The program doesn't really crash, it just closes without reporting an error (I just issued a fix, reinstall the binaries to apply).

The issue with your tree is the presence of bootstrap support values, used by many programs but NOT a part of the Newick tree format. HyPhy interprets them as internal node names. I've also modifed this behavior in the fix, so you should be able to open the tree.

Sergei

Title: Re: Open a tree file... crashes Hyphy
Post by lu on Aug 2nd, 2013 at 5:13pm
Thank you very much Sergei.
Everything works great!

Lu

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