Losing particles upon re-extraction w/o downsampling

Particle Picking
1

I am running into a problem when re-extracting particles. My box size is 512 but during initial processing steps I down sample 2x by setting the “Fourier-crop to box size” to 256. After some pre-processing, I have ~400,000 particles I want to re-extract without downsampling. It set up the job with my particle set and all the micrographs I used originally, with box size set to 512. But the job only returns ~300,000 particles.

I went back through the processing and looked for duplicated particles and went so far as to re-process the data from the beginning. But, I still ended up the the same issue of mysteriously dropped particles upon re-extraction.

I can’t figure out why I am losing ~25% of my particles or if it’s user error, an issue with CryoSparc, or and issue with data placement/our server.

2

Welcome to the forum @segarka. Please can you post the outputs of these commands for both downsampled and non-downsampled cases:

csprojectid=P99 # replace with actual project ID
csjobid=J199 # replace with id of the extract job
cryosparcm cli "get_job('$csprojectid', '$csjobid', 'job_type', 'version', 'status',  'params_spec', 'errors_run', 'input_slot_groups')"
cryosparcm eventlog $csprojectid $csjobid | tail -n 60