Trouble Importing Micrographs to Directory Outside of Cryosparc Folder

Import and Export
1

Hello,

I have been having some trouble with importing micrographs on Cryosparc. Whenever I try to run the import movies job, I get the following error message:

Error1
Error11920×1012 114 KB

When I navigate to each of the directories shown, cryosparc should have reading and writing permissions, as shown below.

mjmcleod@thornextalcomp:/media/mjmcleod/sata_sdd/CryosparcTest/P9/J1$ ls -l
total 160
-rwxrwxr-x 1 mjmcleod mjmcleod    18 Jun 24 12:57 events.bson
drwxrwxr-x 2 mjmcleod mjmcleod 32768 Jun 24 12:56 gridfs_data
drwxrwxr-x 2 mjmcleod mjmcleod 32768 Jun 24 12:57 imported
-rwxrwxr-x 1 mjmcleod mjmcleod 15088 Jun 24 12:57 job.json
-rwxrwxr-x 1 mjmcleod mjmcleod   583 Jun 24 12:57 job.log

mjmcleod@thornextalcomp:~/cryosparc/undergrads$ ls -l
total 13717728
-rw-rw-r--  1 mjmcleod mjmcleod 2681112370 Jan 11 01:14 cuda-repo-ubuntu2004-11-6-local_11.6.0-510.39.01-1_amd64.deb
-rw-rw-r--  1 mjmcleod mjmcleod 2681112370 Jan 11 01:14 cuda-repo-ubuntu2004-11-6-local_11.6.0-510.39.01-1_amd64.deb.1
drwxrwxr-x  2 mjmcleod mjmcleod       4096 Feb 17  2018 empiar_10025_subset
-rw-rw-r--  1 mjmcleod mjmcleod 8684697600 Jun 22 13:44 empiar_10025_subset.tar
drwxrwxr-x 38 mjmcleod mjmcleod       4096 Jun 21 11:35 P5

I’ve also tried to use the command cryosparcm cli "update_project_directory('P9', '/media/mjmcleod/sata_sdd/CryosparcTest/P9')" , but it gives me the following output:

mjmcleod@thornextalcomp:~$ cryosparcm cli "update_project_directory('P9', '/media/mjmcleod/sata_sdd/CryosparcTest/P9')"
Traceback (most recent call last):
  File "/home/mjmcleod/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/mjmcleod/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/mjmcleod/cryosparc/cryosparc_master/cryosparc_compute/client.py", line 92, in <module>
    print(eval("cli."+command))
  File "<string>", line 1, in <module>
  File "/home/mjmcleod/cryosparc/cryosparc_master/cryosparc_compute/client.py", line 65, in func
    assert 'error' not in res, f"Encountered error for method \"{key}\" with params {params}:\n{res['error']['message'] if 'message' in res['error'] else res['error']}"
AssertionError: Encountered error for method "update_project_directory" with params ('P9', '/media/mjmcleod/sata_sdd/CryosparcTest/P9'):
ServerError: Traceback (most recent call last):
  File "/home/mjmcleod/cryosparc/cryosparc_master/cryosparc_command/command_core/__init__.py", line 150, in wrapper
    res = func(*args, **kwargs)
  File "/home/mjmcleod/cryosparc/cryosparc_master/cryosparc_command/command_core/__init__.py", line 3295, in update_project_directory
    assert expanded_new_project_dir not in expanded_all_project_dirs, "Project directory %s already exists/used" % expanded_new_project_dir
AssertionError: Project directory /media/mjmcleod/sata_sdd/CryosparcTest/P9 already exists/used

If I make a new folder (in this case titled P9.2) and run the same command, I get the following output:

mjmcleod@thornextalcomp:~$ cryosparcm cli "update_project_directory('P9', '/media/mjmcleod/sata_sdd/CryosparcTest/P9.2')" 
None

and the import movies job still returns the same error.

Any help on how to fix this error would be appreciated!

2

Welcome to the forum @aboukas.
The permissions look good to me. Please can you post the output of this command:
stat -f /media/mjmcleod/sata_sdd/CryosparcTest/P9/J1

1 Like
3

Thanks for responding @wtempel, here’s what it outputs:

(base) mjmcleod@thornextalcomp:~$ stat -f /media/mjmcleod/sata_sdd/CryosparcTest/P9/J1
  File: "/media/mjmcleod/sata_sdd/CryosparcTest/P9/J1"
    ID: 80000000000 Namelen: 1530    Type: msdos
Block size: 32768      Fundamental block size: 32768
Blocks: Total: 67092480   Free: 23308217   Available: 23308217
Inodes: Total: 0          Free: 0
4

Please can you check whether a filesystem of this type supports/permits the creation of symbolic links? cryoSPARC requires project directories to permit the creation of symbolic links.

1 Like
5

The SSD mounted on /media/mjmcleod/sata_sdd is formatted as a FAT32/vfat file system, which I don’t think supports symbolic links. Is the only way to run cryosparc on that directory to change the file system type? Additionally, whenever I would try to run cryosparcm downloadtest, the download would fail halfway through and the same thing would happen whenever I would download datasets from EMPIAR onto that directory. Is this error also related to the FAT32/vfat file system?

6

It’s the only way that I am familiar with.

Could there be a file or volume size limitations that are exceeded by some EMPIAR datasets?

2 Likes
7

Thanks for all your help! I changed the file system type to ext4 and now both cryosparc and the EMPIAR downloading works.

1 Like