Assertion Error during Local Motion Correction

Motion Correction
1

Hi I’m running cryoSPARC v3.3.1+211214 and on a larger local motion correction job (~7500 images) I’m getting an assertion error:

[CPU: 738.3 MB] Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 85, in cryosparc_compute.run.main
File “cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_local.py”, line 519, in cryosparc_compute.jobs.motioncorrection.run_local.run_local_motion_correction
AssertionError

On smaller jobs with local motion correction in the same version I don’t get this error. Has anyone seen this before or have any ideas?

Bryan

2

@hansenbry What type of non-local motion correction and other jobs did the data undergo, in which sequence, before being input to local motion correction? Did local motion correction fail on the first movie?

3

@wtempel I used Patch motion (multi) CTF correction, classification, and refinements on the data. The local motion correction fails around 2900 images into it

4

@hansenbry Can you identify a specific point in the input sequence that may have been corrupted and at which a job of this type consistently fails?

5

HI @wtempel sorry it took me so long to respond. I was doing some troubleshooting and needed to wait for the outputs to finish. It wasn’t consistent on when it would fail. The inputs were coming from cryoSPARC-Live though. So I thought maybe if I ran motion correction again on the data first that might fix the issue and it did. I took the cryoSPARC-Live output and did patch motion correction again then did local motion with the particles I had identified and it went through without error.

6

Have the same problem with patch motion correction performed in CryoSPARC live v3.3.2+220518. Linking the exported exposures to a local motion correction job fails with

Error occurred while processing S1/import_movies/000_Nov03_18.51.33.tif
Traceback (most recent call last):
File “/Local/app/cryosparc/cryosparc2_worker/cryosparc_compute/jobs/pipeline.py”, line 60, in exec
return self.process(item)
File “cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_local.py”, line 221, in cryosparc_compute.jobs.motioncorrection.run_local.run_local_motion_correction_multi.motionworker.process
File “cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_local.py”, line 233, in cryosparc_compute.jobs.motioncorrection.run_local.run_local_motion_correction_multi.motionworker.process
File “cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_local.py”, line 234, in cryosparc_compute.jobs.motioncorrection.run_local.run_local_motion_correction_multi.motionworker.process
File “cryosparc_worker/cryosparc_compute/jobs/motioncorrection/motioncorrection.py”, line 110, in cryosparc_compute.jobs.motioncorrection.motioncorrection.motion_correction
AssertionError

Marking as incomplete and continuing…

Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 85, in cryosparc_compute.run.main
File “cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_local.py”, line 362, in cryosparc_compute.jobs.motioncorrection.run_local.run_local_motion_correction_multi
AssertionError: First exposure failed with exception: <cryosparc_compute.jobs.pipeline.PipelineExceptionResult object at 0x7fb631ba9190>

Connecting the same micrographs from a non-live patch motion correction job works fine.

7

@mannda Have you since updated CryoSPARC and are still seeing this problem?

8

Things work fine since ~v4.11+230104
Thank you very much :slight_smile: