Topaz in cryosparc error

Troubleshooting
1

Hello,
I did the following to use topaz in cryosparc but I get the error below when I run the topaz train job in cryosparc. How do I get topaz to work in cryosparc?

  1. source /home/cryosparc_user/anaconda3src-4topaz-bashrc
  2. conda create -n topaz python=3.6
  3. source activate topaz
  4. The Topaz executable I use in cryosparc
    ~/anaconda3/envs/topaz/bin/topaz
  5. firefox http://localhost:39000

ERROR:

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_compute/jobs/topaz/run_topaz.py”, line 113, in run_topaz_wrapper_train
topaz_version = utils.get_topaz_version(topaz_exec_path)
File “cryosparc2_compute/jobs/topaz/topaz_utils.py”, line 60, in get_topaz_version
process = subprocess.Popen([topaz_exec_path, ‘–version’], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True)
File “/home/cryosparc_user/cryosparc_software/cryosparc2_worker/deps/anaconda/lib/python2.7/subprocess.py”, line 394, in init
errread, errwrite)
File “/home/cryosparc_user/cryosparc_software/cryosparc2_worker/deps/anaconda/lib/python2.7/subprocess.py”, line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

2

Hi @Dominique,

This error indicates that the job cannot find the Topaz executable. Based on the information provided, I think three possible causes for this are:

  1. The Topaz installation commands were never run in the new environment.
  2. Topaz was installed in an environment with Python 3.6 when cryoSPARC runs on Python 2.7.
  3. The input Topaz executable path is incorrect.

First ensure that the Topaz installation commands were run in Anaconda environment. These commands can be found here https://github.com/tbepler/topaz.

If this is not the case, try installing Topaz in an environment with Python 2.7.

Finally if the above two don’t work, double check to ensure the input path is correct. Instructions for finding the path can be found here https://cryosparc.com/docs/tutorials/topaz/.

Regards,
Jay Yoo

3

Thank You @jyoo !

I installed anaconda in my home directory and which python gives me
/anaconda3/bin/python which is not found. Removing / finds anaconda3/bin/topaz executable that works in cryosparc. That and changing to 2.7. Its running now, Thanks!

Best,
Dominique