I have installed Topaz into cryosparc and topaz train is working fine. But when I run Topaz extract, I met an OS error.
[CPU: 277.5 MB Avail: 131.84 GB]
Starting Topaz process using version 0.2.5a…
[CPU: 277.5 MB Avail: 131.87 GB]
Using preprocessed micrographs from J158/preprocessed
[CPU: 282.8 MB Avail: 131.97 GB]
Found 23581 processed micrograph(s) in /sdf/group/cryoem/g/CT90/HD3/20250626/CS-hd3/J158/preprocessed
[CPU: 282.8 MB Avail: 131.97 GB]
An additional 1 micrograph(s) require preprocessing. Results will be saved to /sdf/group/cryoem/g/CT90/HD3/20250626/CS-hd3/J158/preprocessed
[CPU: 283.4 MB Avail: 131.97 GB]
[CPU: 283.4 MB Avail: 131.97 GB]
Starting preprocessing…
[CPU: 283.4 MB Avail: 131.97 GB]
Starting micrograph preprocessing by running command /sdf/group/cryoem/g/CT90/conda/envs/topaz/bin/topaz preprocess --scale 10 --niters 200 --num-workers 8 -o /sdf/group/cryoem/g/CT90/HD3/20250626/CS-hd3/J158/preprocessed [1 MICROGRAPH PATHS EXCLUDED FOR LEGIBILITY]
[CPU: 283.4 MB Avail: 131.97 GB]
Preprocessing over 2 processes…
[CPU: 285.5 MB Avail: 131.61 GB]
usage: topaz preprocess [-h] [-s SCALE] [–affine] [–sample SAMPLE]
[CPU: 285.5 MB Avail: 131.61 GB]
[–niters NITERS] [-a ALPHA] [-b BETA] [–metadata]
[CPU: 285.5 MB Avail: 131.61 GB]
[-d DEVICE] [-t NUM_WORKERS] [-j NUM_THREADS]
[CPU: 285.5 MB Avail: 131.61 GB]
[-o DESTDIR] [–format FORMAT_] [-v]
[CPU: 285.5 MB Avail: 131.61 GB]
files [files …]
[CPU: 285.5 MB Avail: 131.64 GB]
topaz preprocess: error: the following arguments are required: files
[CPU: 283.7 MB Avail: 131.96 GB]
Preprocessing command complete.
[CPU: 283.7 MB Avail: 131.96 GB]
Preprocessing done in 6.174s.
[CPU: 283.7 MB Avail: 131.96 GB]
Inverting negative staining…
[CPU: 286.9 MB Avail: 131.95 GB]
Inverting negative staining complete.
[CPU: 286.9 MB Avail: 131.95 GB]
[CPU: 286.9 MB Avail: 131.95 GB]
Starting extraction…
[CPU: 286.9 MB Avail: 131.96 GB]
Starting extraction by running command /sdf/group/cryoem/g/CT90/conda/envs/topaz/bin/topaz extract --radius 8 --threshold -6 --up-scale 10 --assignment-radius -1 --min-radius 5 --max-radius 100 --step-radius 5 --num-workers 8 --device 1 --model /sdf/group/cryoem/g/CT90/HD3/20250626/CS-hd3/J158/models/model_epoch02.sav -o /sdf/group/cryoem/g/CT90/HD3/20250626/CS-hd3/J161/topaz_particles_prediction.txt [11791 MICROGRAPH PATHS EXCLUDED FOR LEGIBILITY]
[CPU: 288.7 MB Avail: 131.95 GB]
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main
File “/app/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py”, line 1182, in run_topaz_wrapper_extract
utils.run_process(extract_command)
File “/app/cryosparc_worker/cryosparc_compute/jobs/topaz/topaz_utils.py”, line 71, in run_process
process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True, text=True)
File “/app/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/subprocess.py”, line 971, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File “/app/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/subprocess.py”, line 1863, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
OSError: [Errno 7] Argument list too long: ‘/sdf/group/cryoem/g/CT90/conda/envs/topaz/bin/topaz’