I set a accumulational prune step. You can only prune it on a trained model. Using the same .cfg file and some prune params like:
[convolutional]
prune=1 //enable prune
prune_threshold_min=0.0001 //start prune threshold
prune_threshold_max=0.0005 //end prune threshold
prune_add_step=5000 // each epoch add (prune_threshold_max-prune_threshold_min)/prune_add_step
batch_normalize=1
filters=16
size=3
stride=1
pad=1
activation=leaky