OSError: I/O error

3D Refinement
1

Dear community,
I got the below error when running the NUF refiinement after reextracting particls and unbinned them.

" 0SError: I/0 error, mrc readmic (l) line 977: Invalid argument. The requested frame/particle cannot be accessed. The file may be corrupt, orthere may be a mismatch between the file and its associated metadata (i.e. cryosparc .cs file)
I/0 request details.filename: /ssdcache/instance b-login:39001/links/551-J1589-1746507608/35048a05929fd0b0e2916dbfo4fbf91ecf761c.mrc
data type: 0x10frames.[14:15]
eer upsample factor:2
eer number of fractions: 40 "

Does anyone knows the reason and solution for this problem.
Many thanks,
Ge

2

I think you are somehow “looking” for the old particles (EER upsample) while providing the new ones? try rerunning a clean NU-refinement? try running check for corrupt particles job? I’m not sure why NU-refinement would be looking for .mrc…

3

@geyang928 Aside from the suggestions by @CryoEM2, you may also try:

  1. clone the failed refinement job
  2. then, in the new job, disable Cache particle images on SSD
    image
    image668×228 10 KB
  3. then run the new job

The new job is expected to run slowly, due to the lack of particle caching. Its completion or failure could nevertheless help narrow down the search for a cause of the I/O error.