Topaz extraction issue

[guodong]

[wtempel]

Welcome to the forum @guodong .
Please can you post

1. post text instead of the screenshot.
   You can obtain the text of the (end of the) event log with the command

   cryosparcm eventlog P1 J590 | tail -n 50
   

2. the outputs of these commands

   cryosparcm cli "get_job('P1', 'J590', 'version', 'type', 'params_spec', 'started_at')"
   cryosparcm cli "get_job('P1', 'J513', 'version', 'type', 'params_spec', 'started_at')"
   cryosparcm eventlog P1 J513 | grep "Starting Topaz"
   

[guodong]

n 2025 16:14:44 GMT] [CPU RAM used: 224 MB] Starting Topaz process using version 0.2.5…
[Wed, 18 Jun 2025 16:14:44 GMT] [CPU RAM used: 224 MB] Using preprocessed micrographs from J513/preprocessed
[Wed, 18 Jun 2025 16:14:44 GMT] [CPU RAM used: 225 MB] Found 2530 processed micrograph(s) in /beagle3/eozkan/cryosparc_guodongxie/projects/NCAM1RIG3_FOM/CS-ncam1rig3ecd/J513/preprocessed
[Wed, 18 Jun 2025 16:14:44 GMT] [CPU RAM used: 225 MB] An additional 0 micrograph(s) require preprocessing. Results will be saved to /beagle3/eozkan/cryosparc_guodongxie/projects/NCAM1RIG3_FOM/CS-ncam1rig3ecd/J513/preprocessed
[Wed, 18 Jun 2025 16:14:44 GMT] [CPU RAM used: 225 MB] --------------------------------------------------------------
[Wed, 18 Jun 2025 16:14:44 GMT] [CPU RAM used: 225 MB] No micrographs require preprocessing. Skipping.
[Wed, 18 Jun 2025 16:14:44 GMT] [CPU RAM used: 225 MB] Inverting negative staining…
[Wed, 18 Jun 2025 16:14:44 GMT] [CPU RAM used: 225 MB] Inverting negative staining complete.
[Wed, 18 Jun 2025 16:14:44 GMT] [CPU RAM used: 225 MB] --------------------------------------------------------------
[Wed, 18 Jun 2025 16:14:44 GMT] [CPU RAM used: 225 MB] Starting extraction…
[Wed, 18 Jun 2025 16:14:44 GMT] [CPU RAM used: 225 MB] Starting extraction by running command /beagle3/eozkan/topaz.sh extract --radius 16 --threshold -6 --up-scale 7 --assignment-radius -1 --min-radius 5 --max-radius 100 --step-radius 5 --num-workers 4 --device 0 --model /beagle3/eozkan/cryosparc_guodongxie/projects/NCAM1RIG3_FOM/CS-ncam1rig3ecd/J513/models/model_epoch10.sav -o /beagle3/eozkan/cryosparc_guodongxie/projects/NCAM1RIG3_FOM/CS-ncam1rig3ecd/J590/topaz_particles_prediction.txt [2530 MICROGRAPH PATHS EXCLUDED FOR LEGIBILITY]
[Wed, 18 Jun 2025 16:19:31 GMT] [CPU RAM used: 226 MB] Extraction command complete.
[Wed, 18 Jun 2025 16:19:31 GMT] [CPU RAM used: 226 MB] Starting particle pick thresholding by running command /beagle3/eozkan/topaz.sh convert -t 0 -o /beagle3/eozkan/cryosparc_guodongxie/projects/NCAM1RIG3_FOM/CS-ncam1rig3ecd/J590/topaz_particles_prediction_thresholded.txt /beagle3/eozkan/cryosparc_guodongxie/projects/NCAM1RIG3_FOM/CS-ncam1rig3ecd/J590/topaz_particles_prediction.txt
[Wed, 18 Jun 2025 16:19:35 GMT] [CPU RAM used: 226 MB] Particle pick thresholding command complete.
[Wed, 18 Jun 2025 16:19:35 GMT] [CPU RAM used: 226 MB] Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 116, in cryosparc_master.cryosparc_compute.run.main
File “/software/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py”, line 1204, in run_topaz_wrapper_extract
assert particles_extracted, “No particles extracted. Possible causes include 'Particle threshold' parameter being too high or a version discrepancy between the Topaz or PyTorch instance that trained the model and the one that is being used for extraction.”
AssertionError: No particles extracted. Possible causes include ‘Particle threshold’ parameter being too high or a version discrepancy between the Topaz or PyTorch instance that trained the model and the one that is being used for extraction.

[guodong]

cryosparcm cli “get_job(‘P1’, ‘J590’, ‘version’, ‘type’, ‘params_spec’, ‘started_at’)”
{‘_id’: ‘685070bbb9b8e5d067102141’, ‘params_spec’: {‘exec_path’: {‘value’: ‘/beagle3/eozkan/topaz.sh’}, ‘par_diam’: {‘value’: 150}}, ‘project_uid’: ‘P1’, ‘started_at’: ‘Wed, 18 Jun 2025 16:14:39 GMT’, ‘type’: ‘topaz_extract’, ‘uid’: ‘J590’, ‘version’: ‘v4.6.0’}

[wtempel]

Thanks for posting the information for job J590. Please can you also post information for the ancestor job J513, which you can obtain with the commands

cryosparcm cli "get_job('P1', 'J513', 'version', 'type', 'params_spec', 'started_at')"
cryosparcm eventlog P1 J513 | grep "Starting Topaz"