Hi Mustansar,
If you run your Sakai server with auto.ddl=true your database should be updated automatically once tomcat starts.
On the other hand, what beta are you using for your Sakai 2.9 server? The last time we tried out the tool on 2.9 it was on 2.9-b2 and it run ok. But after that there were some changes on Sakai that broke the tool. We decided to wait until a more stable version for Sakai 2.9 were released. So, even though the tool has been tested and it works for 2.9, by now there is no guaranty that it will work with no errors.
Jesus Federico