Since both are false, you never read the output from the command. If there are a few lines of output before the script bp_genbank2ff3.pl generates any files, it might just wait for the (line oriented) output buffer to be empty before continuing (I don't know exactly without trying it out, but seems a reasonable assumption). You can check that easily by just removing the if clause , i.e. just do this

# if ( $print_to_stdout || defined $output_fh ) {
    while (<$command_out>) {
        print if ($print_to_stdout);
        print $output_fh $_ if ( defined $output_fh );
    }
#}
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