Ab-Initio Reconstruction error

3D Reconstruction
1

Hi,
I found the following error when I ran Ab-Initio Reconstruction(5 classes, C1).

Traceback (most recent call last):
** File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main**
** File “cryosparc_master/cryosparc_compute/jobs/abinit/run.py”, line 302, in cryosparc_master.cryosparc_compute.jobs.abinit.run.run_homo_abinit**
** File “/spshared/apps/cryosparc/cryosparc_worker/cryosparc_compute/noise_model.py”, line 119, in get_noise_estimate**
** assert n.all(n.isfinite(ret))**
AssertionError

2

v4.7.1 cryosparc version

3

@biolender Please can you try running clones of the failed abinit job with the following alternative parameter changes and let us know whether any of the changes (a) allow a given abinit job to complete and (b) produce useful volumes:

  1. set Noise model (white, symmetric or coloured) to white .
  2. or set both Enforce non-negativity and Center structures in real space to False .
  3. or reduce the Number of Ab-Initio classes to 4 or, if the job fails with 4, 3.
4

Thanks, I will have a try. Besides, when I set the Number of Ab-Initio classes to 3, it worked. This also happened to my other datasets. I didn’t use the micrograph denoiser for these datasets, so I’m not sure whether it is related.