Error with Import Particle Stack job in cryoSPARC v3.2 (particles.star from Relion v3.1)

Troubleshooting
1

Import particle stack from Relion 3.1 works perfectly fine in cyroSPARC v3.1 After updating to v3.2, it throws the following error message. Any hint?

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main
File “/home/spuser/apps/cryosparcV2/cryosparc2_master/cryosparc_compute/jobs/imports/run.py”, line 339, in run_import_particles
level, all_base_paths, abs_to_rel_map, all_rel_paths = symlink_all_abs_files_to_import_dir(proj_dir_abs, job_dir_rel, all_abs_paths)
TypeError: symlink_all_abs_files_to_import_dir() missing 1 required positional argument: ‘uid_to_path_map’

2

We see this also! Although only on one dataset so far, haven’t figured out the cause yet

3

same here, running on 3.2.0+210622.
The problem did not occur with patch 210615

4

Can confirm - for us it also happened only after the most recent patch, and cloning an import job which ran successfully using the previous patch results in failure on the current patch

5

@team is there any patch in the works for this? we currently can’t import particle stacks which is a bit of a limitation, but it seems there is no way to downgrade to the previous patch without breaking things? Just wondering if I should bite the bullet and reinstall or wait for a fresh patch

6

Hey everyone,

Thank you for reporting, and sorry for any inconvenience. This is indeed a bug that was created by the patch- we will release a fix for this in the next patch tomorrow.
In the meantime, we have removed the patch from the list of patches that can be applied.
You can roll back the updates from this patch by running cryosparcm patch --force

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7

wow that was quick, thanks @stephan!

8

Hey everyone,

A new patch is available that replaces the patch which introduced this bug. Sorry again for any inconvenience!

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