FileNotFoundError: [Errno 2] during Movie Import

Install, Configure and Update
1

Hi I have gotten this error while importing movies of a new dataset:
It finds the correct number of movies to import, but then fails with this error:

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main
File “/home/cryosparcuser/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/imports/run.py”, line 863, in run_import_movies_or_micrographs
level, all_base_paths, abs_to_rel_map, all_rel_paths = symlink_all_abs_files_to_import_dir(proj_dir_abs, job_dir_rel, abs_paths_to_import, uid_to_path_map)
File “/home/cryosparcuser/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/imports/run.py”, line 763, in symlink_all_abs_files_to_import_dir
abs_to_rel_map, all_rel_paths = symlink_paths(proj_dir_abs, os.path.join(job_dir_rel, import_dir_name), all_abs_paths, all_base_paths, uid_to_path_map)
File “/home/cryosparcuser/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/imports/run.py”, line 750, in symlink_paths
os.symlink(abs_path, dest)
FileNotFoundError: [Errno 2] No such file or directory: /path/to/raw/movies → /path/to/imported/movies

I’m not if this is related or not but I recently updated to v4.7 and while doing so the worker node failed to update, so I updated it manually following the cryosparc guide. I didn’t notice any errors while do so, so I thought everything was fine… but i guess not.

any help would be great!
/Ben

2

I tried to Force-reinstall the master and worker dependencies. with cryosparcm forcedeps and cryosparcw forcedeps. both ran to completion without errors.

I also tried reconnecting the worker node as described here: Cryosparc tries to run worker in old directory, cannot find - #2 by nfrasser

neither solved this problem :frowning:

3

Hi Ben,

Please can you post the outputs of these commands:

csprojectid="P99" # substitute actual project ID
csjobid="J999" # substitute import job ID
cryosparcm cli "get_job('$csprojectid', '$csjobid', 'job_type', 'version',  'params_spec', 'errors_run')"
df -Th $(cryosparcm cli "get_project_dir_abs('$csprojectid')")
4

thanks for the fast reply!
here are the outputs:

{'_id': '6818b0be2465d8788a4f6297', 'errors_run': [{'message': "[Errno 2] No such file or directory: '/media/cryosparcuser/…/RAW_DATA/k3_frames_a/Images-Disc1/GridSquare_1474882/Data/FoilHole_1504051_Data_1476433_2_20250503_001044_fractions.tiff' -> '/media/cryosparcuser/…/CS-dbb01412/J50/imported/004778679295542336332_FoilHole_1504051_Data_1476433_2_20250503_001044_fractions.tiff'", 'warning': False}], 'job_type': 'import_movies', 'params_spec': {'accel_kv': {'value': 300}, 'blob_paths': {'value': '/media/cryosparcuser/…/RAW_DATA/k3_frames_a/Images-Disc1/GridSquare_*/Data/FoilHole_*.tiff'}, 'cs_mm': {'value': 2.7}, 'gainref_path': {'value': '/media/cryosparcuser/…/RAW_DATA/gainref_counted.mrc'}, 'psize_A': {'value': 0.65}, 'total_dose_e_per_A2': {'value': 40}}, 'project_uid': 'P74', 'uid': 'J50', 'version': 'v4.7.0'}

Filesystem     Type   Size  Used Avail Use% Mounted on
/dev/sde1      ntfs3   17T   13T  4,2T  75% /media/cryosparcuser/…
5

Have you previously imported data to a CryoSPARC project directory on this disk? I am not sure whether the required symlink operation is supported on an ntfs3 filesystem.

6

hmm thanks.
yes i have 2 other data sets on that disk that imported just fine previously. I usually use ntfs without issues…

but now that you mentioned that, I checked and it seems the drive is corrupted! Strange, I did not notice any issues, I could read and write files like normal…

Thanks! I would have probably spent a lot of time troubleshooting that. I will reformat the drive, copy the data back and try again.