Multiple-arg system() doesn't quite work like that (read this). Redirection using the shell metacharacter ">" is handled by the shell, which reads the entire string "program $ref_file > $outfile", parses it, and executes the command with redirection.

When you do multiple-arg system, you're going raw and skipping the shell (usually). Redirections have to be performed manually and you'll lose some convenience you get with using a shell. Example:

sub executeComm {
    my ($outfile, @comm) = @_;

    print "cmd: <", join("> <" => @comm), ">\n";

    # manual redirection - dup(2) STDOUT first
    open(my $ORIGSTDOUT, ">&" . fileno(*STDOUT)) or die $!;
    open(*STDOUT, ">", $outfile) or die $!;

    # run it!
    my $exit = system @comm;

    # restore STDOUT
    open(*STDOUT, ">&=" . fileno($ORIGSTDOUT)) or die $!;

    print "exit: ", $exit, "\n";
}

print "before\n";
executeComm($outfile, $program, $ref_file);
print "after\n";
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If you really want a quick-and-dirty fix for your "whitespace-in-filename" problem, place single-quotes around the filenames, as in:

executeComm ("program '$ref_file' > '$outfile'");
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Now make sure you don't have single-quotes in the filenames...