The transformation step can take quite some time depending on the operations you're doing Adarsh, like complex joins and other types of calculations.
It's difficult to say withouth seeing the application, but i would assume that your transforming a high amount of data and to me, 35 minutes isn't that high for the transformation part.
Compare your question to this: "My road train is loaded up and good to go but when I start my 5000 mile journey the last trailer is dragging my entire truck to a very slow speed. What could be the problem? You cannot look at my truck or inspect the insides or the loaded goods."
Pretty darn impossible to comment on your problem without resorting to general suggestions. Please try to provide a few more details about the last step and its environment, the reference execution speed and how it differs in practice, the script complexity, the amount of tables and records, the machine on which it is expected to run with acceptable speed, etc. Thanks.