FileNotFoundError: [Errno 2] No such file or directory in MotionCor2

Motion Correction
1

Dear all,

I need your invaluable help and experience. I know that a similar problem already arose and has been discussed/solved in the past, but I’m not able to solve it myslef:

I’m using the last cryoSPARC version (4.2.0) and I want to use the last MotionCor2 version (1.6.3). When I try to run the job, I get this error message:

Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 96, in cryosparc_compute.run.main
  File "/home/agwilson/Software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_motioncor2.py", line 397, in run_motioncor2_wrapper
    global_shifts = parse_global_alignment(full_frame_log_abs)
  File "/home/agwilson/Software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_motioncor2.py", line 21, in parse_global_alignment
    with open(full_frame_alignment_log) as logfile:
FileNotFoundError: [Errno 2] No such file or directory: '/home/agwilson/HP018/221207_Wilson_HAS32/CS-cmv-gp48-spd-cs-processing/J47/motioncor2_logs/00-Patch-Full.log'

I saw in another discussion that a similar issue was solved with a soft link of the movies inside the cryosparc project directory, I already tried without success.

I saw in the MotionCor2 building step this message:
Path to MotionCor2 executable. Run cryosparcm cli 'set_project_param_default(project_uid, 'exec_param', path)' (where project_uid is your project number (e.g ‘P12’) and path is the absolute path to the MotionCor2 executable) to keep this parameter consistent across this project.
I tried the command but I only got “SyntaxError: invalid syntax”.

Do you have any idea how I could resolve this issue?
Thank you in advance for your help and attention.
Best,
Andrea

2

From my experience, cryoSPARC doesn’t work well with the new versions of MotionCor. The highest version that seems to be working is 1.4.5.

3

@daddea Support for newer versions of MotionCor2 is on our roadmap for a future software release.

1 Like
4

Thank you so much for the reply @wtempel .

So it’s a problem related to support, I’m not doing any stupid error?

5

@daddea It seems that the newer version of MotionCor2 organizes its output differently from older versions, and the current release of CryoSPARC is not (yet) aware of these changes.