After clearing intermediate result, re-extract particles report error

Troubleshooting
#1

Hi,
After I clear intermediate result of all job, I can’t extract particles. It report an error as the follwing:

[CPU: 252.9 MB] Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main
File “/opt/cryosparc2/cryosparc_worker/cryosparc_compute/jobs/extract/run.py”, line 97, in run_extract_micrographs_multi
particles_dset.add_fields(rc.com.get_dataset_columns(‘particle.blob’, ‘blob’))
AttributeError: ‘NoneType’ object has no attribute ‘add_fields’

Is the intermediate result essential for next job? Doesn’t the final result file include all parameters for next job?

Cryosprac v3.0.1

Lei

Thank you!

#2

Hi @Lei,

Is it possible if you can post your workflow? Which job did you get the particles from?
As a note, the “Clear Intermediate Results” job only clears the intermediate results of iterative jobs (2D Classification, Refinement, etc., ). It won’t affect jobs that create micrographs or particle picking jobs.

#3

I have been running into the same issue. I get the problem for any job that was present when i cleared intermediate results. This is includes extraction from any 3D jobs (ab initio, homo-, hetero-, non-uniform, and local refinements). If I clear the job in which I am linking the particles from and rerun the job with all intermediate jobs present, the re-extraction of particles does not work also.

EDIT: After messing around and trying to track down the issue, it appears that using the micrograph output from a curated micrographs job that has the intermediate files cleared, seemed to be my issue. Using the micrograph output from patch ctf fixed the issue.

#4

Hi @kyestachowski,

Thank you for your report. It led to us finding the real culprit, which was a bug in the Curate Exposures job. A fix for this will be released in the next version of cryoSPARC (v3.1).

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#5

@kyestachowski We have released a v3.1.0 update to cryoSPARC in which this issue should be resolved. Please let us know if this issue persists in v3.1.0.

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