about "iteration"of -evaluate about igor HOT 1 CLOSED

Dear @decenwang ,
As mentionned in this section -infer and -evaluate trigger the exact same actions (at least for now) since using -evaluate IGoR performs the Expectation step of the Expectation-Maximization algorithm (note: the Expectation step is computationally intensive in our setting while the Maximization one is close to instantaneous), while using -infer -N_iter N IGoR will perform N EM steps. In a nutshell -evaluate is the same as -infer -N_iter 1.
The two different commands exist only for the sake of clarity for users using pre-defined recombination models and to allow for future improvements in the model inference strategy without retro-compatibility issues for command line users.

To answer your final question, yes you should use evaluate using -evaluate -set_custom_model /your/working/dir/inference/final_parms.txt /your/working/dir/inference/final_marginals.txt
As a shortcut you could directly use 6 iterations of EM and would get the same result as explained above, though this is not guaranteed to work in future releases of IGoR

from igor.