RELION

RELION is an open source cryoEM data processing suite. It is implemented here through SBGrid.

Starting up

There are two ways to run RELION on the Blanca cluster.

Sbatch submission

RELION is built with HPC integration in mind, so it can submit sbatch scripts for you and makes them easy to write inside the GUI. (underlying templates are found at /projects/biokem/software/biokem/users/src). To start, allocate an interactive job with minimal resources to run the GUI on Blanca, start the GUI, and then Submit to queue:

biokem-interactive
cd /path/to/data/folder
sbgrid
relion

Now in the Running tab:

  • Set Submit to queue to Yes

  • Defaults should be auto populated (Walltime can be up to 168:00:00)

  • If you want to submit to Blana at large:

    • Queue name = blanca

    • QoS = preemtable

    • Account = blanca-biokem

    • Walltime = 24:00:00 (or less)

You can submit multiple jobs at the same time using this method. You can use the GUI to moniter the output of each job.

Interactively

When starting interactively, you must allocated all of the resources you need before starting the GUI. Example:

biokem-interactive -c 24 -g 1 -m 48
cd /path/to/data/folder
sbgrid
relion

The drawbacks with this method are:

  • Need to know how many resources you will use beforehand

  • Only way to allocate more resources is to exit screen and start over

  • Need to keep terminal alive while processing (24hr limit)

  • Have to wait until resources become available to start jobs

  • Sequesters idle resources from other users

RELION OTF

Similar to CryoSPARC’s Live function, RELION can also preprocess data as it is being transferred into your folder using Schedules (See here).