system("script.sh >> filename");
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calls the shell interpreter under the hood, something that can be very inconvenient (and even dangerous). For instance, the script arguments have to be properly quoted or they could be wrongly splitted by the shell

An alternative way to redirect the output for the called program is to reopen STDOUT:

open my $oldout, ">&STDOUT"
  or die "Can't dup STDOUT: $!";
open STDOUT, ">", $fn
  or die "Can't open $fn: $!";

system $script, @args;

open STDOUT, ">&", $oldout;
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Or on Unix/Linux systems, you can use fork and exec instead of system and perform the redirection after the fork:

my $pid = fork;
if (defined $pid and $pid == 0) {
  open STDOUT, ">", $fn or die;
  exec $script, @args;
  exit 1;
}
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