PhiSpy 3.2 problems

[joanna...@gmail.com]

Hello,
I am currently working on S.aureus environmental strains in which I want to find prophage sequences. I've tried PhiSpy 3.2 recently and encountered a few problems:
- I don't obtain a prophage.tbl file in an output directory but a lot of temp.fasta files instead,
- I am not sure about the results in prophage_tbl.txt file as the final status of a lot of genes is O, e.g. integrase, phage terminase and portal protein being normally recognized as prophage-like genes. Actually, in the column viii - my status - the software returns the value 1 in many of these cases but afterwards column x - final status - is 0. Moreover, even when column vii - (rank of each gene provided by random forest) gives the same value for two analyzed genes (e.g. 0.26), my rank is equal to 1 and classification is the same (0 or 1), the final status is not the same, it can be 0 or 1 and I don't understand this,
- I obtain empty columns xi-xvi each time (starts and ends of att).
I would be thankful for any help.
Best,
Joanna