I recently ran Topaz train, Topaz extract, and now I trying to extract the particles. I had to separate my data into two sets for Topaz to work, but with each set the particle extraction gets about two thirds of the way through before it starts failing.
This is the error I get below.
Error occurred while processing micrograph J79/motioncorrected/013727141603375834819_FoilHole_23962683_Data_23954576_23954578_20221124_171009_Fractions_patch_aligned_doseweighted.mrc
Traceback (most recent call last):
File “/s/em/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 60, in exec
File “/s/em/cryosparc_worker/cryosparc_compute/jobs/extract/run.py”, line 485, in process
path_abs = os.path.join(proj_dir_abs, micrograph[‘background_blob/path’])
Marking J79/motioncorrected/013727141603375834819_FoilHole_23962683_Data_23954576_23954578_20221124_171009_Fractions_patch_aligned_doseweighted.mrc as incomplete and continuing…
I have tried running with 1 and 2 GPU’s. I have previously been able to extract particles with blob picker and template picking from the exact same dataset, the only different being is I didn’t have to split the micrographs into two sets for the picking to run.
We are on version 4.2.1.
Any solutions or suggestions as to what is going on? We’re struggling to understand the error message or why it’s happening.