Local Refinement Stuck After Unbinning

Local Refinement
1

Hello,

I am running a Local Refinement job in CryoSPARC. When I used a 360-pixel box size, the refinement completed successfully. However, after the refinement reached the Nyquist limit, I unbinned the particles to the original 720-pixel box size and started another Local Refinement. The job appears to get stuck at the following point:

[CPU: 53.05 GB]
Running local cross validation for A...

The job does not appear to progress beyond this point. I need to run the refinement using the unbinned 720-pixel box because the 360-pixel refinement has already reached the Nyquist limit.

Could you please let me know what I can do to resolve this issue? Thank you very much!

2

Welcome to the forum @fwang . What version of CryoSPARC do you use? Was this job queued to a cluster-type (as opposed to node-type) lane?

3

Thank you so much for your reply! The version is v4.7.1. Yes. The job was submitted to the nova cluster-type lane through the SLURM scheduler.

4

Thanks @fwang Please can you post the outputs of these commands:

project_uid=P99 # replace with actual project ID
job_uid=J999 # replace with job ID of stuck local refine job
cat $(cryosparcm cli "get_job_dir_abs('$project_uid', '$job_uid')")/queue_sub_script.sh
cryosparcm joblog $project_uid $job_uid | tail -n 20
5

Thank you very much for your suggestion. Do you know where can I find the outputs of these commands?

I reduced the box size from 720 pixels to 560 pixels, and now the local refinement runs successfully without hitting the Nyquist limit. I’m still curious why the 720-pixel refinement would not run~ Thank you very much!

6

The commands would need to be run in a Linux shell on the CryoSPARC master host. The outputs’ text would be displayed in the shell window.