2D classification fails!

2D Classification
1

I recently used the CrYOLO 1.9.1 particle stack to extract particles from my micrographs. Later I started a 2D classification job on the extracted particles from the “Extract Micrographs” job. The 2D classification failed with this error.
Is this because of the CrYOLO Particles or something different?
We use the v4.1.2 of CryoSPARC .

I have pasted the error message screenshot below.

image
image1920×1144 209 KB

The Text Inside the error is as follows :
[2023-03-08 11:15:56.65]
[CPU: 1.72 GB Avail: 998.31 GB]
Traceback (most recent call last):
File “/home/c/cryospar/cryosparc_worker/download/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 2061, in run_with_except_hook
run_old(*args, **kw)
File “cryosparc_master/cryosparc_compute/engine/cuda_core.py”, line 131, in cryosparc_compute.engine.cuda_core.GPUThread.run
File “cryosparc_master/cryosparc_compute/engine/cuda_core.py”, line 132, in cryosparc_compute.engine.cuda_core.GPUThread.run
File “cryosparc_master/cryosparc_compute/engine/engine.py”, line 1101, in cryosparc_compute.engine.engine.process.work
File “cryosparc_master/cryosparc_compute/engine/engine.py”, line 390, in cryosparc_compute.engine.engine.EngineThread.find_and_set_best_pose_shift
File “<array_function internals>”, line 5, in unravel_index
ValueError: index 1043808007 is out of bounds for array with size 336

[2023-03-08 11:15:56.65]
[CPU: 1.72 GB Avail: 998.31 GB]
Traceback (most recent call last):
File “/home/c/cryospar/cryosparc_worker/download/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 2061, in run_with_except_hook
run_old(*args, **kw)
File “cryosparc_master/cryosparc_compute/engine/cuda_core.py”, line 131, in cryosparc_compute.engine.cuda_core.GPUThread.run
File “cryosparc_master/cryosparc_compute/engine/cuda_core.py”, line 132, in cryosparc_compute.engine.cuda_core.GPUThread.run
File “cryosparc_master/cryosparc_compute/engine/engine.py”, line 1101, in cryosparc_compute.engine.engine.process.work
File “cryosparc_master/cryosparc_compute/engine/engine.py”, line 390, in cryosparc_compute.engine.engine.EngineThread.find_and_set_best_pose_shift
File “<array_function internals>”, line 5, in unravel_index
ValueError: index 1036543000 is out of bounds for array with size 336

Thank You

2

Welcome to the forum @karthik.
Please can you paste the text inside the screenshot you posted as text to facilitate searches of forum discussions, and let us know version and patch level of your CryoSPARC instance.
Thanks.

3

Sure. Thank You @wtempel . I will do the needful. Ill edit my post and share all the details.

4

Please can you test the following:

  1. Does the error also occur when you run a clone of this failed job with caching disabled?
  2. Are there any errors reported when you run a check for Corrupt Particles job with Check for NaN Values enabled?
5

Thank you @wtempel .

  1. Yes the error occurred even after disabling the caching option.

  2. There were 11 particles that were having some problems, I then took the output from this job (the check corrupt particles job) and ran a 2D classification, and it worked like a charm.

Thank you once again for the help. Much appreciated. :smile: :raised_hands:

6