Topaz 2D Class problem




I followed the Topaz Tutorial and finally I wanted to make a 2D classification with the default options. The job stops with the following error:

Job ready to run

Using random seed of 722128966
Loading a ParticleStack with 316142 items…
Windowing particles
Using 50 classes.
Computing 2D class averages:
Volume Size: 32 (voxel size 2.99A)
Zeropadded Volume Size: 64
Data Size: 220 (pixel size 0.44A)
Using Reconstruction Resolution: 6.00A (15.0 radius)
Using Alignment Resolution: 6.00A (15.0 radius)
Windowing only corners of 2D classes at each iteration.
Using random seed for initialization of 2015500313
Done in 0.755s.
Start of Iteration 0
Traceback (most recent call last):
File “cryosparc2_compute/jobs/”, line 1490, in run_with_except_hook
run_old(*args, **kw)
File “cryosparc2_worker/cryosparc2_compute/engine/”, line 110, in
File “cryosparc2_worker/cryosparc2_compute/engine/”, line 111, in
File “cryosparc2_worker/cryosparc2_compute/engine/”, line 1072, in
File “cryosparc2_worker/cryosparc2_compute/engine/”, line 392, in cryosparc2_compute.engine.engine.EngineThread.find_and_set_best_pose_shift
ValueError: invalid entry in index array

The 2D classification using the template picker on the same dataset runs fine.
What could be the problem?
Version 2.12.4


Memory issues on cluster

Hi @wlugmayr1,

This is a known issue that will be resolved in the next release of cryoSPARC.

When the release comes, the same “Topaz Train” job can be used but the “Topaz Extract” and “Extract from Micrographs” jobs will have to be repeated.

Jay Yoo