SNAP gene predictor training fails.

[MmasterT]

The do_snap flag in reat prediction only works if we add a pre trained hmm model, otherwise the pipeline fails. Also, we alwas should set as default the -lcmask flag in --snap_extra_params to treat the lowercased text as masking for the predictions.

The issue seems to be a wrong input for the hmm-assembler.pl where we are using a File as the species param and not a string as it should be.