Particle extraction not detecting imported micrographs

Import and Export
1

Hi,
I am attempting to extract sub particles from a set of imported micrographs. I have done this before using this same data set and I am going back attempting it with a new mask. However, when I run the extract from micrographs job, the job returns the following error for every micrograph:

Traceback (most recent call last):
File “/blue/rmckenna/apps/cryosparc/cryosparc_worker/cryosparc_compute/jobs/extract/run.py”, line 165, in run_extract_micrographs_cpu_parallel
_, mrcdata = mrc.read_mrc(path_abs, return_psize=True)
File “/blue/rmckenna/apps/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 177, in read_mrc
with open(fname, ‘rb’) as file_obj:
FileNotFoundError: [Errno 2] No such file or directory: ‘/blue/rmckenna/j.zachary/AAV2/CS-aav2-fab2a-local/J1/imported/004600951273575709283_FoilHole_6603854_Data_6581253_0_20240507_150446_aligned_DW.mrc’

Error while reading micrograph /blue/rmckenna/j.zachary/AAV2/CS-aav2-fab2a-local/J1/imported/004600951273575709283_FoilHole_6603854_Data_6581253_0_20240507_150446_aligned_DW.mrc; skipping and continuing…

Any help would be appreciated.

2

Is the path shown a symbolic link whose target is is no longer available?

stat /blue/rmckenna/j.zachary/AAV2/CS-aav2-fab2a-local/J1/imported/004600951273575709283_FoilHole_6603854_Data_6581253_0_20240507_150446_aligned_DW.mrc
stat -L  /blue/rmckenna/j.zachary/AAV2/CS-aav2-fab2a-local/J1/imported/004600951273575709283_FoilHole_6603854_Data_6581253_0_20240507_150446_aligned_DW.mrc
3

Hi,

I’m not overly familiar with all the terminology, but if I understand your question correctly, the files are still present at that pathway and I can access them via my terminal, but cryosparc is unable to recognize them.

4

@jfz002 I neglected to request that you run these commands

and post the commands’ outputs here. This may help us figure out the problem.

5

Got it.

stat /blue/rmckenna/j.zachary/AAV2/CS-aav2-fab2a-local/J1/imported/004600951273575709283_FoilHole_6603854_Data_6581253_0_20240507_150446_aligned_DW.mrc
File: /blue/rmckenna/j.zachary/AAV2/CS-aav2-fab2a-local/J1/imported/004600951273575709283_FoilHole_6603854_Data_6581253_0_20240507_150446_aligned_DW.mrc → /blue/rmckenna/shared/Stanford/L41/micro/FoilHole_6603854_Data_6581253_0_20240507_150446_aligned_DW.mrc
Size: 103 Blocks: 8 IO Block: 4096 symbolic link
Device: bac98d24h/3133771044d Inode: 1206967829690075008 Links: 1
Access: (0777/lrwxrwxrwx) Uid: ( 3174/rc-svc-rmckenna-web) Gid: ( 3128/rmckenna)
Access: 2024-12-11 13:35:13.000000000 -0500
Modify: 2024-12-11 13:35:13.000000000 -0500
Change: 2024-12-11 13:35:13.000000000 -0500
Birth: 2024-12-11 13:35:13.000000000 -0500

stat -L /blue/rmckenna/j.zachary/AAV2/CS-aav2-fab2a-local/J1/imported/004600951273575709283_FoilHole_6603854_Data_6581253_0_20240507_150446_aligned_DW.mrc
stat: cannot statx ‘/blue/rmckenna/j.zachary/AAV2/CS-aav2-fab2a-local/J1/imported/004600951273575709283_FoilHole_6603854_Data_6581253_0_20240507_150446_aligned_DW.mrc’: No such file or directory

6

@jfz002 On import, to preserve disk capacity, imported files are linked, not copied into the job directory. In your case, the link inside the job directory points to a file inside
/blue/rmckenna/shared/Stanford/L41/micro/ outside the project directory, but that file or the entire directory seem to be no longer available.
You may want to try:

  • making the files available again under
    /blue/rmckenna/shared/Stanford/L41/micro/
  • or, if the files are now available under a different path, adjusting the symbolic links