We have picked particles with cisTEM and are now doing the "Refine Pkgs" step before moving to 2D classification. We are running it on a cluster, but it this steps takes a really long time (estimated time around 1 hour for about 300k particles). It seems a lot and we wanted to check if it's a typical time or if there's something wrong with our setting or submission.
Also, it looks like this particular task is not submitted to the queue of the cluster but is run locally. Is there a way to submit it or any way to make this step faster?