I am not sure about this, but are you able to redirect the output? 
system("sort somefile.txt >somefile2.txt") or die;

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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 2>error.txt") or die;

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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!

In reply to Re: System(), writing to a new file by zork42
in thread System(), writing to a new file by cyates

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