> open(FILE,'|httrack $URL -O /tmp/test/$SiteId -
> m1000000M50000000nN4q');
> Then the output will be sended to the user's email 
account 
> as an email. This is very annoying if I am using cron to 
> run the perl script every minute, because my email 
account 
> will be flooded with these kind of messages.

Isn't it possible to do:
open(FILE,'|httrack $URL -O /tmp/test/$SiteId - 
m1000000M50000000nN4q >/dev/null');
?
Besides you should add the two keywords:
--quiet

To avoid any input request.