Topaz extract running issue


When I run the Topaz extract job, it gives this error:
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/”, line 93, in
File “/opt/cryosparc3/cryosparc_worker/cryosparc_compute/jobs/topaz/”, line 1127, in run_topaz_wrapper_extract
File “/opt/cryosparc3/cryosparc_worker/cryosparc_compute/jobs/topaz/”, line 70, in run_process
process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True, text=True)
File “/opt/cryosparc3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/”, line 858, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File “/opt/cryosparc3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/”, line 1704, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
OSError: [Errno 7] Argument list too long: ‘/opt/miniconda3/envs/topaz/bin/topaz’

The path is correct, but I don’t get what “argument list too long” means?!!

You need to split your dataset - it fails with more than ~4000 images.

Just use Exposure Sets to split into smaller groups, then run Topaz Extract on each (and then you can combine the outputs for particle extraction).


Thank you so much! Can I split them after Topaz train and then do the Topaz extract? Because the train part is already done.

yes, it is just for topaz extract

Thank you! I faced another problem, after Topaz extract, I ran particle extraction, and now that I run 2D classification job, I get this error:
AssertionError: Non-optional inputs from the following input groups and their slots are not connected: particles.ctf. Please connect all required inputs.

I also tried to make one particle stack from 4 I got from my Topaz extract job, it still fails.

I would guess you extracted from micrographs from a Patch Motion job? you need to extract from mics with CTF estimates (e.g. after Patch CTF or CTFFIND)