CryoSPARC v2.13.0 failed on Ab-Initio Reconstruction and Heterogeneous Refinement

Troubleshooting
1

Hi, I updated to v2.13 yesterday on my workstation with running centos-release-7-6.1810.2.el7.centos.x86_64 and got the following errors respectively when I set 3 for number of Ab-Initio classes and used 6 Volumes for Heterogeneous Refinement:

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/abinit/run.py”, line 385, in cryosparc2_compute.jobs.abinit.run.run_homo_abinit
File “cryosparc2_compute/dataset.py”, line 379, in subset_idxs
newdata[field] = self.data[field][keep_idxs]
ValueError: could not broadcast input array from shape (14) into shape (90)

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/hetero_refine/run.py”, line 457, in cryosparc2_compute.jobs.hetero_refine.run.run_hetero_refine
File “cryosparc2_compute/dataset.py”, line 379, in subset_idxs
newdata[field] = self.data[field][keep_idxs]
ValueError: could not broadcast input array from shape (1021) into shape (6000)

When I set 1 for number of Ab-Initio classes, cryoSPARC worked. I had to downgrade to v2.12.4 in order to make Heterogeneous Refinement work.

Thanks a lot in advance!

2

Hi @donghuachen,

Thank you very much for the detailed error report!
We have identified the issue and we’re going to be deploying a patch update within the next few minutes. I’ll keep you posted.

3

Hi @donghuachen

We have released an update to cryoSPARC that fixes the issues you’re having (v2.13.2, January 30, 2020).

To update, run: cryosparcm update

4

Thanks for your quick update!