Import Micrographs broken in 2.12?

Troubleshooting
20

Hi @jcfromme, @crescalante, @DanielAsarnow, @alexmag, @mplockhartuom, @scaiola, @CBEN, @ABehal2020, @user123, @drawoliver,

This bug has been (actually) fixed! Update to cryoSPARC v2.12.4 (cryosparcm update) to get the latest fixes, which include:

New:

  • Exposure Groups Utility Updates
    • Create exposure groups using regular expressions and separators
    • Test your exposure group creation strategy
  • 3D Variability updates to default parameters: create better results without tweaking

Fixed:

  • Multiprocessing jobs (Patch CTF, Patch motion, Full-frame motion) fail with abnormal termination errors
  • Import micrographs and import movies function incorrectly with exposure groups
  • Imported jobs with inputs cause the tree layout to fail or throw an error
  • 3D Variability display "intermediate" mode outputs are incorrectly scaled
  • 3D Variability display "cluster" mode outputs contain no particles
5 Likes
21

And it works! Thank you :heart_eyes:

1 Like
22

Great, Thank you!:heart:

1 Like
23

Seem to be working for me too.

Thank you for the fixes

24

Many thanks! Import Micrographs is working fine now.

25

It is working. Thank you

26

I updated to v2.12.4 a couple days ago and have been getting this error while importing .mrc files that I converted from .ser files with e2proc2d.py
This error was not thrown while I was using these files in earlier versions of cryoSPARC

KeyError: ‘skip_header_check’

27

Hey @armbrustered,

Can you please restart cryosparcm restart then run cryosparcm cli "refresh_job_types()"?

28

I updated to V2.12.4, but the bug "KeyError: ‘skip_header_check’ " still exists.

I have run cryosparcm restart and cryosparcm cli "refresh_job_types()". The following characters appear：

image
image1690×855 66.8 KB

29

Hi @Peiyu-Xu,

Can you confirm you’re creating a new job and not cloning the original job that caused the issue?

If that doesn’t work, can you make sure there are no zombie processes:

cryosparcm stop
ps -ax | grep “supervisord” (kill only the process that is running from your cryosparc2 install)
ps -ax | grep “cryosparc2_command” (kill all the matching processes related to your cryosparc2 instance)
ps -ax | grep “mongod” (kill only the process running your cryosparc2 database)

e.g. kill 82681
1 Like
30

@stephan looks like those zombie processes were the main cause of this as *.mrc upload issue as well as other issues (such as topaz particle picker not showing up after an update, with the main issue likely being connected to spawn errors that show up during cryosparcm start). Everything is working now after killing the cryosparc jobs found with ps -ax | grep “supervisord”

Thanks for your help!

31

@stephan Just wondering, in general is it safe to kill mongod? I’ve been using mongod --shutdown with the db connection parameters, but kill is easier to remember :slight_smile:

32

Hey @DanielAsarnow,

It should be fine:
https://docs.mongodb.com/manual/tutorial/manage-mongodb-processes/#use-kill

1 Like
34

HI
I still have same problem with KeyError: ‘override_exp_group_id’
my cryosparc version is 2.13.2

35

Hi @KSJ,

Did you try running with a brand new job? Did you also make sure to check that there were no zombie processes?

36

yes
I’ve run a number of files, some of which work, some of which have errors.
Examples of error file are EMPIAR-10059, EMPIAR-10240

37

I also met the some problem, In cryosparc v2.14.2. When I started a new job in an old project, cryosparc reported “project_uid” and it failed start. Creating new job also not work. I tried to restart cryosparc master, killed the zombie process (supervisord?), but it still reported the same error. I downgraded cryosparc to v2.11 and it successed to run new job. Is there still a bug here?

38

Hi @sunny1226,

Could you paste the full error traceback you received? It can help us better understand what went wrong.

- Suhail

39

Oh sorry… I have just fully reinstalled the instance (including the database) recently because of “exporting project” notifications cannot be cleared. And now everything seems fine. I guess there is a database corruption?

40

Hi @sunny1226,

You can clear notifications in the Notification Manager (found in the Resource Manager) by clicking the “clear” button next to the notification. More information can be found here: https://cryosparc.com/docs/tutorials/data-management

Also, if you are still seeing your projects and jobs (and can log into cryoSPARC) your database is most likely not corrupted.