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HYPHY Package >> HyPhy bugs >> GA analysis: ModelSelectorBranchLocal.bf inputs http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1165360880 Message started by Sarah on Dec 5th, 2006 at 3:21pm |
Title: GA analysis: ModelSelectorBranchLocal.bf inputs Post by Sarah on Dec 5th, 2006 at 3:21pm
I'm having trouble with the inputs expected by ModelSelectorBranchLocal.bf (the download of 11/21). First I'm prompted to choose a genetic code. I type "1" and then receive "Please choose an option." I type "1" again (or sometimes just hit enter) and then am asked to choose a codon file to analyze. I enter the file and am then prompted again to choose a codon file. If I enter the same file I then receive "This doesn't seem to be a valid Newick string file..." I've played around and sometimes entered the tree at this step, and then hit return when prompted for the tree. Then I'm asked to choose an evolutionary model two times and then the program appears to start running. If I don't enter the tree in advance, I tend to get an error message.
I'd love to write a script for these inputs once I understand what's expected. I've had the same problem executing these commands via a terminal window from both a Mac and a Windows machine. Sarah |
Title: Re: GA analysis: ModelSelectorBranchLocal.bf input Post by Sergei on Dec 5th, 2006 at 3:36pm
Dear Sarah,
Not sure where this is coming from. The file REQUIRES an MPI environment to run though, so this could be the issue. Make sure you download a more recent version of the GA branch files, since the original one was missing some necessary files. Here's an example session on my cluster: Code (] [sergei@monkey_supreme HYPHY_Source):
Cheers, Sergei |
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