I am not sure about this, but are you able to redirect the output?
in reply to System(), writing to a new file
If I've remembered my unix syntax, the following will send any error messages (on STDERR) to the file "error.txt"
system("sort somefile.txt >somefile2.txt") or die;
IIRC you must use the single argument version of system() for redirections to work. (I think the multiple argument versions bypass the shell.) I'd check this though!
system("sort somefile.txt >somefile2.txt 2>error.txt") or die;