CS deep picker error

Particle Picking
1

Hi,
I have try to use CS deep picker and got this error:

 Traceback (most recent call last):
  File "cryosparc_worker/cryosparc_compute/run.py", line 84, in cryosparc_compute.run.main
  File "cryosparc_worker/cryosparc_compute/jobs/deep_picker/run_deep_picker.py", line 255, in cryosparc_compute.jobs.deep_picker.run_deep_picker.run_deep_picker_train
AssertionError: No particles corresponding to input micrographs were found. Ensure that non-zero particle picks were input and that the particle picks are from the input micrographs.

when using the same input for topaz it work.

Best,

2

Hi @Elad,

Thanks for reporting – were the input particles originally picked in cryoSPARC, and if so, with which job (i.e. template, blob, etc.)? Also, what were the parent jobs for the particles input and the micrographs input?

Best,
Michael

3

Hi Michael,

thanks for you replay.

The input particles were picked in CS with template and then cleaned by 2D. The particles from the selected classes were used for the deep picker.

The parent jobs were particles–> select 2d, microgrphs --> curate Exposures.

Best,

4

Hi @Elad,

Apologies for the delay. May I ask what the Number of parallel threads parameter was set to? If you are still running into errors with this job, could you try setting this parameter to 1, and re-running the job? Please let me know if that helps.

Best,
Michael

5

it was run with 10 parallel threads.