When I'm running standalone blast with my genome against the phage database I'm getting an output file with 5000 hits. I've sorted out the excel sheet with evalue lower than 0.01 query cover >= 70℅ and ℅id >= 30 . Now ,after doing all this my output data reduced to 289 hits. Well, I don't think that my genome will have 289 phage genes. How to go further from here ? Please help me ...
What you are doing (what blast can mainly do) is "Searching homologous genes". With my understanding, what you want to do is "Gene prediction". I recommend you to google with the term "gene" "prediction" or such.
If you want to do something with your current result, I think many genes are mapped on the same region on your genomes, filter out such overlapped hits.
From the command line you can type blastp -help. This will show you all of the available options. So, if you just want the top hit five hit you can you the option, -max_target_seqs 5 in the blastp command line. If you just want the top hit replace the 5 with a 1. Is this what you were looking for??