I've successfully installed and run HyPhy on my Mac OS 10.3 and am now interested in running it on a separate Unix box from the command line. I'm following the online HyPhy guide about how to create a batch file. I've created one that runs fine, however in the output (messages.log) it tells me:

Row and/or column partition is empty. All the data will be used by default.

If I understand this correctly, it means that it didn't read my data partition that I put in the batch file using the "CreateFilter" command.  ??? Am I interpreting this message correctly? I've compared my batch file against the documentation several times, and cannot figure out what I am doing wrong. Here is the line from my batch file:

DataSetFilter myFilter = CreateFilter (rre,1,"2,5,29,32,41,47,53,56,68,77,101,122,128,137,158,161,164,170,182,188,200"
,"");

At this point, I can't figure out if the problem is me or the program. We just had the latest version of HyPhy installed this past week, so it should be a current version.

Any suggestions are most appreciated!