Error running Local refine with subtracted particles

Local Refinement
1

Hello all,

I am running into an error shown below. Essentially, I had a particle stack that I performed global non-uniform refinement on followed by particle subtraction of specified regions. Using Homogeneous Reconstruction only, I was able to successfully run the job and saw the removal of the specific regions. However, when I then used the particle stack, map and mask from the reconstruction job for a new Local Refinement job I receive the error below. It is unclear to me what Values it is now missing. Any help is appreciated.

Thanks,
Wil

Traceback (most recent call last):
File “/lsi/local/pkg/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 2294, in run_with_except_hook
run_old(*args, **kw)
File “/lsi/local/pkg/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/threading.py”, line 953, in run
self._target(*self._args, **self._kwargs)
File “cryosparc_master/cryosparc_compute/engine/newengine.py”, line 2714, in cryosparc_master.cryosparc_compute.engine.newengine.process.work
File “cryosparc_master/cryosparc_compute/engine/newengine.py”, line 2766, in cryosparc_master.cryosparc_compute.engine.newengine.process.work
File “cryosparc_master/cryosparc_compute/engine/newengine.py”, line 1518, in cryosparc_master.cryosparc_compute.engine.newengine.EngineThread.compute_error
ValueError: Detected NaN values in newengine.compute_error. 11294500 NaNs in total, 500 particles with NaNs.

2

@salmen Please can you provide additional details:

  1. What version of CryoSPARC do you run?
  2. Does the same error occur when Cache particle images on SSD is disabled?
  3. Does the same error occur when you
    • run a Check Particles job with Check for NaN values enabled for the input particles of the failed local refinement job
    • then run a local refinement job using as input the particles output by the Check Particles job?