Hello! I am experiencing a TypeError when running a Topaz Train job in CryoSPARC v. 5.0.0
The IT person that installed Topaz mentioned that there were previous issues configuring the Topaz wrapper and have turned the troubleshooting over to me. I am pretty new to CryoSPARC, so any and all help would be very appreciated! We are using Topaz v. 0.2.5a
Thank you in advance!
Here is the error log:
TypeError: concat() takes 1 positional argument but 2 were givenTraceback (most recent call last):
File “cli/run.py”, line 105, in cli.run.run_job
File “cli/run.py”, line 210, in cli.run.run_job_function
File “/cryosparc/cryosparc_worker/compute/jobs/topaz/run_topaz.py”, line 544, in run_topaz_wrapper_train
utils.run_process(rc, split_command)
File “/cryosparc/cryosparc_worker/compute/jobs/topaz/topaz_utils.py”, line 143, in run_process
assert process.returncode == 0, f"Subprocess exited with status {process.returncode} ({str_command})"
^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: Subprocess exited with status 1 (/opt/miniconda3/envs/topaz/bin/topaz train_test_split --number 7 --seed 304822133 --image-dir /DATA/rawdata/Current_Projects/project/screening/J457/preprocessed /DATA/rawdata/Current_Projects/project…)
Welcome to the forum @ah.user2026. Please can you post the end of the job log, which you can display with the command
cryosparcm job log P99 P199
where P99, J199 need to be replaced by the Topaz Train job’s actual project and job IDs, respectively.
I am using the web application, so I downloaded the full job log from that. Here is the log from the error on. Thank you!
2026-03-03 08:40:23,457 core run ERROR | Encountered exception!
Traceback (most recent call last):
File “cli/run.py”, line 105, in cli.run.run_job
File “cli/run.py”, line 210, in cli.run.run_job_function
File “/cryosparc/cryosparc_worker/compute/jobs/topaz/run_topaz.py”, line 544, in run_topaz_wrapper_train
utils.run_process(rc, split_command)
File “/cryosparc/cryosparc_worker/compute/jobs/topaz/topaz_utils.py”, line 143, in run_process
assert process.returncode == 0, f"Subprocess exited with status {process.returncode} ({str_command})"
^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: Subprocess exited with status 1 (/opt/miniconda3/envs/topaz/bin/topaz train_test_split --number 7 --seed 304822133 --image-dir /DATA/rawdata/Current_Projects/project/screening/J457/preprocessed /DATA/rawdata/Current_Projects/project…)
2026-03-03 08:40:29,366 core monitor INFO | ========= monitor detected main process exit.
2026-03-03 08:40:29,369 core monitor INFO | ========= monitor process now complete.
Thanks @ah.user2026 . To troubleshoot the failure of the topaz train_test_split command, you may want to
- Confirm that the
topaz preprocess step inside CryoSPARC job J457 succeeded.
- Run the full
topaz train_test_split command on the command line (under the designate Linux account that “owns” the CryoSPARC instance and its processes) und examine the command’s output. If the command is truncated inside the job log, you may need to “reconstruct” the full command by referring to the topaz tutorial for the relevant Topaz version (v0.2.5a link).
and adapting the tutorial command to your job’s path and parameters.
