Topaz extract running issue

Troubleshooting
1

Hi,

When I run the Topaz extract job, it gives this error:
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 93, in cryosparc_compute.run.main
File “/opt/cryosparc3/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py”, line 1127, in run_topaz_wrapper_extract
utils.run_process(extract_command)
File “/opt/cryosparc3/cryosparc_worker/cryosparc_compute/jobs/topaz/topaz_utils.py”, 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/subprocess.py”, 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/subprocess.py”, 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?!!

2

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).

Cheers
Oli

3

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

4

yes, it is just for topaz extract

5

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.

6

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)