Hello,

I am trying to run a likelihood analysis using the GY94_3x4 model matrix which comes with the hyphy package. Upon running my batch file, however, I always receive the error message as follows:

Error:
Operation 'MAccess' is not implemented/defined for a Number

Function call stack
1 : Branch  under condition ModelGeneticCode[h]==10 to 9 else 12
-------
2 : codonfreq=GUIBuildCodonFrequencies(observedFreq_outer)


I have tried several other codon models as well and the same error (more or less) is returned for each.

In my troubleshooting efforts, I tried to use a codon model formatted by the GUI rather than the ones in the trunk directory. Interestingly, I found that the "buildcodonfrequencies" function included in the model file that the GUI returns does not work but the other/standard buildcodonfrequencies model works fine with that matrix.

Any thoughts? I've attached my batch file as well.