The solution is very simple. Make sure you have the following line in the CMakeLists.txt.

add_dependencies(reef_estimator ${catkin_EXPORTED_TARGETS})

1. Make sure the targets that are being build is configured to ALL_TARGETS. Target should be All targets.
2. The executable must be the name of your program, and should match the executable name of the CMake file.
3. The working directory must be /home/your_user_name/catkin_ws. Or wherever you have the catkin workspace.

Thanks and Good Luck!