Hi, I've written a perl program which makes a system call to a program called 'Predator' (for the biologists among you it's a protein secondary structure prediction program). You run Predator from the command line as follows:
/path/to/Predator/predator -foutput_file.txt input_file.txt
where Predator reads from input_file.txt and writes the results to output_file.txt. If you miss out -foutput_file.txt the results are written straight to screen.
My system call in my perl program therefore looks like this:
system "/home/rebecca/bs127/Predator/predator -fpredator.txt input_seq
However, this doesn't work - predator.txt is not created. There's definitely not a problem opening input_sequence.txt, because this is used successfully elsewhere in the program.
Predator works on input_sequence and creates predator.txt when run from the command line.
What could the problem be? I'm assuming it's permissions of some sort, but don't know enough about them to see what. Any ideas?