Have you read this? It is in the documentation

Using non human/worm/fly genomic DNA

At the moment, genewise only has gene frequency files for human and worm sequences. The production of these files are based around somewhat annoying and non portable script. In any case, making a data set requires allot of effort as it needs to be clean

The consequence of all this is that the species that you are comparing against (eg, hamster) may not have a gene frequency (.gf) file. In which case you basically have two options Use a close species - i.e., for hamster, use human or rat Use -splice flat -intron tied which switches the splice model to ``start at GT, finish at AG'' with no other information

As noted on the Wise2 site, for most cases Wise2 can be replaced by Exonerate, for GeneWise replacement see http://www.ebi.ac.uk/~guy/exonerate/beginner.html#protein2genome

Also the current version of Wise2 is 2.4.1, so you might want to upgrade (for Debian based systems a package is available, see: http://packages.debian.org/sid/wise). Support for Wise2 is available from the author.