Argument list too long! topaz extraction error!

Particle Picking
1

Hi,

I am getting the following error while running topaz extraction

[CPU: 298.5 MB Avail: 104.38 GB]
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main
File “/usr/local/cryosparc/2.0/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py”, line 1182, in run_topaz_wrapper_extract
utils.run_process(extract_command)
File “/usr/local/cryosparc/2.0/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 “/usr/local/cryosparc/2.0/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 “/usr/local/cryosparc/2.0/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: ‘/opt/topaz/0.2.5.11.8/bin/topaz’

2

Split your dataset into smaller sets of micrographs (<~4000 mics each) and run separate Topaz Extract jobs for each, then combine outputs. This has apparently been fixed in the latest version of Topaz, but I am not sure yet if that is compatible with cryoSPARC, so for now this is the workaround.

3

I don’t know how to split into smaller sets of micrographs though.

4
5

Thanks a lot! I got it.

6

I have split my dataset and run Topaz extract job for each. However, after combining the outputs , program doesn’t allow me to run 2D classification or heterogeneous refinement.

Output : Cryosparc job aborted abnormally.

7

You need to extract the particles - topaz extract only gives locations. You need to use extract from micrographs afterwards.

8

I did it too, however, something wrong with combining the output I guess. do you use the set exposure tool for the combining the outputs or introduce all the particles as separate output to 2D or heterogeneous refinement job ?

9

Combining the outputs and providing as input to extract from micrographs should work fine. Is extract from micrographs giving an error?

10

I understand now. Previously, I performed separate topaz extractions and did individual extractions for each of them, then tried to combine them for the downstream job. Thanks a lot!

11

Individual extractions should also work - presuming you are extracting from the right micrographs? You should be performing Topaz extract and Extract from Micrographs on micrographs that have CTF estimates, e.g. from Patch CTF.

12

Thanks ! I figured out the problem.

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