Backticks (or qx//) capture output to STDOUT, but not to STDERR. For an easy solution, see Capture::Tiny.

Update: For example (adapted from the documentation):

use Capture::Tiny ':all';

my $cmd  = ...
my @args = ...

print "Start of my code\n";

my ($stdout, $stderr, $exit) = capture
{
    system($cmd, @args);
};

print "Exit status is : $exit\n";

if ($exit)
{
    print "Error in executing command : $stderr\n";
    exit;
}

print $stdout;
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Hope that helps,