If you could post the output, and properly the script used to run, then I might be able to give you a hint.
The first iteration of all calculation is very long since it is here that it tabulated and calculates the non-local part of the hamiltonian, once this first iteration is completed, it will continue at normal speed, so perhaps has your calculation not stopped, but is doing the non-local part of the hamiltonian for the NEGF part of the calculation.
