Hi Prateek,
I believe this particular DTP is taking more time because for the set of records it is fetching, logic in transformation is taking longer.
I suppose you are reading lot of data from other targets as well in transformation field/start/end routine.
If you are not using Semantic Group key in DTP, consider using this option. This may drastically reduce the time of execution.
apart from this, also consider the design improvement suggested by others.
hope this helps,
Purvang