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?
3

Sorry for the late response. Thank you for giving me these points.

  1. Version 4.5.3+240807
  2. I have rerun the local refine job without the Cache particles on SSD and the same error appears
  3. I have also tried running Check particles with the input particles, which did not identify any NaN values and then using the output particles from the Check particles job to local refinement job still caused the same error.
4

Hello All,

I was searching through the older troubleshooting posts and realized my issue is the same as this linked post.

Based on the previous post, I tried rerunning my job using all the same settings except switching refine_scale_min / “Minimize over per-particle scale” from TRUE to FALSE and it was able to run without throwing an error.

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