Dear Sergel,

Thank you for your immediate response regarding run times.  I have another question.  I keep getting error messages and don't understand why.  I am using a Nexus file which includes aligned nucleotide sequences with a tree and am running HyPhy in OS 10.3.5.  I can run the data in "stripstopcodons" without a problem.  I have problems when I run the file in "dNdSRateAnalysis."  The program runs, but then when it is done and I try to open the out file, I get an error message that says:

Operation: : is not defined.
Current BL Comand:Build Formula:RUNNING
MG94xREV MODEL COMPARISONS on Macintosh HD:
Users:bpsweeney:Desktop:hyphy data:
Trial3US.dat###########3x3
CLASSES###########+--------------------------------------
+------------------------------+----------------------------------+
Current operation/job has been terminated.

Can you tell me what this could mean?

Thank you,

Beatriz

Dear Beatriz,


wrote on Apr 6^th, 2005 at 1:42pm:

Dear Sergel,  The program runs, but then when it is done and I try to open the out file, I get an error message that says: Beatriz

The .out file is a text file; you can view it with your favorite text editor, or use the File->Open->Open Text File command in HyPhy. The error messages you were getting were because HyPhy was assuming that the .out file was a batch file and trying to parse it.

You may also want to use Standard Analyses->Codon Selection Analyses->dNdSResultsProcessor.bf to get even more information (e.g. find positively selected sites etc). This file prompts you to locate the marginals file written out by HyPhy. This file will have .marginals extensions.

HTH,
Sergei