You're right, I must have gotten mixed up in the process. The command works as you indicated. Thank you everyone for your help.

Here's my final working code for completeness

#! /usr/bin/perl

use warnings;
use strict;

use IPC::Run qw(run timeout);

my $from_file   = '/home/product/ftp-temp/long.mov';
my $tmp_to      = '/home/product/ftp-temp/out.wav';
my $in;
my $out;
my $err;

my @cmd = ('/usr/bin/ffmpeg','-y','-i', $from_file, $tmp_to);

eval {
    #16 seconds is long enough to convert about 288 minutes of audio
    #Current server converts about 18 minutes per second of runtime.
    #production version will use custom timeout based on expected
    #lengths of material. 
    run \@cmd, \$in,\$out,\$err, timeout(16, exception=>'timeout');
};

if ($@ =~ /timeout/) {
    print "Timed out...\n\n";
} else {
    print "\n\nCompleted Task\n\n";
}
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