Reference based motion correction - OSError:

Motion Correction
1

Dear colleagues,

An error when just in the very beginning of the Reference Based Motion Correction Protocol
Does anyone have an explanation for that?
What can be the solution?

STARTING: OPTIMIZE HYPERPARAMETERS

[CPU: 1.49 GB Avail: 123.12 GB]

Working with 2206 movies containing 12501 particles
[CPU: 1.49 GB Avail: 123.12 GB]

Computing intended data cache configuration
[CPU: 635.1 MB Avail: 123.97 GB]

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 95, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_reference_motion.py”, line 322, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.run_reference_motion.run_reference_motion_correction
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/refmotion.py”, line 766, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.refmotion.mainfn_param_optimize
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/refmotion.py”, line 674, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.refmotion.prepare_datasets
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/refmotion.py”, line 143, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.refmotion.read_gain_and_defects
File “cryosparc_master/cryosparc_compute/blobio/prefetch.py”, line 70, in cryosparc_master.cryosparc_compute.blobio.prefetch.synchronous_native_read
OSError:

IO request details:
filename: /nas/cold/cryosparc_projects/CS-katharina-110124/J123/imported/20231212_174314_EER_GainReference.gain
filetype: 1
header_only: 0
idx_start: 0
idx_limit: -1
eer_upsampfactor: 2
eer_numfractions: 40
num_threads: 6
buffer: (nil)
buffer_sz: 0
nx, ny, nz: 0 0 0
dtype: 0
total_time: -1.000000
io_time: 0.003638

Thank you.

Kind regards,
Dmitry

2

What is the output of the command

stat /nas/cold/cryosparc_projects/CS-katharina-110124/J123/imported/20231212_174314_EER_GainReference.gain

?

1 Like
4

image
image824×258 144 KB

5

Could this symbolic link be stale (the target file not available)?
What are the outputs of the commands:

readlink -e /nas/cold/cryosparc_projects/CS-katharina-110124/J123/imported/20231212_174314_EER_GainReference.gain
stat -f $(readlink -e /nas/cold/cryosparc_projects/CS-katharina-110124/J123/imported/20231212_174314_EER_GainReference.gain)
1 Like
6

image
image858×139 73 KB

7

Hello @wtempel - I manually checked the gain location, and it seems to have been moved.
I am not sure if I can find it back.
Maybe that was an issue.

I will try to put another reverence to the corresponding location and give it the same name so the system can pick it up.

Thank you.

Kind regards,
Dmitry