This is not strictly a Perl question, but your Perl script may play into it. Please reduce your Perl script to a minimal example that produces that behaviour and post that example. If reducing your Perl script is too complicated, first test if the behaviour is linked to Perl at all by launching other commands in the same way.

As a first step, try launching the following Perl script instead:

#!/usr/bin/perl -w
use strict;

print "Hello world\n";
print "I got the following parameters: @ARGV\n";
[download]

As an aside, you likely shouldn't run research scripts as the root user.