I am running the tutorial from https://github.com/linsalrob/PhiSpy After following the instructions, I ran the command
./PhiSpy.py -i Test_Organism/160490.1/ -o output_directory -t 25
I get the following error message
Making Test Set... (need couple of minutes) cant open file 1 error: Shannon does not work The input organism is too small to predict prophages. Please consider large contig (having at least 40 genes) to use PhiSpy.
I then ran PhiSpy on another RAST annotated genbank directory of another WGS assembly, and I still get the same error message. I have the versions of Python, biopython, gcc and randomForest as per spec.