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.

4

Hello, I am experiencing this error as well. I originally Fourier cropped the particles from 360 to 90 and upon re-extraction without fourier cropping I am getting a frame error. I tried clearing all the old particle extraction jobs. The eer error is a red herring because I’m using tifs from K3 data. I have been using 16 bit data if that makes a difference. I tried doing it without the cached particles as suggested above and ran into the same error, traceback below. Any guidance would be wonderful

I am using version 4.7.1 because I don’t want to update my OS. I’m working on a heterogenous particle set and finally found a particle subset that looks like what I want and I would really prefer not to lose the particles that I found.

Thanks,

Eric

**Traceback (most recent call last):
File “/home/beta/Applications/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 2306, in run_with_except_hook
run_old(*args, **kw)
File “cryosparc_master/cryosparc_compute/gpu/gpucore.py”, line 136, in cryosparc_master.cryosparc_compute.gpu.gpucore.GPUThread.run
File “cryosparc_master/cryosparc_compute/gpu/gpucore.py”, line 137, in cryosparc_master.cryosparc_compute.gpu.gpucore.GPUThread.run
File “cryosparc_master/cryosparc_compute/jobs/class2D/newrun.py”, line 620, in cryosparc_master.cryosparc_compute.jobs.class2D.newrun.class2D_engine_run.work
File “cryosparc_master/cryosparc_compute/engine/newengine.py”, line 566, in cryosparc_master.cryosparc_compute.engine.newengine.EngineThread.read_image_data
File “/home/beta/Applications/cryosparc/cryosparc_worker/cryosparc_compute/ioengine/cmdbuf.py”, line 87, in wait
raise IOError(‘\n\n’.join(errs))
OSError: I/O error, mrc_readmic (1) line 977: Invalid argument
The requested frame/particle cannot be accessed. The file may be corrupt, or there may be a mismatch between the file and its associated metadata (i.e. cryosparc .cs file).

I/O request details:
filename: /run/media/beta/DATA/Eric/CS_Working/CS-bodv-anp32a/J138/extract/BoDV_Host_1_23_26_9704_particles.mrc
data type: 0x10
frames: [9:10]
eer upsample factor: 2
eer number of fractions: 40**

5

@edg42 Please can you post the outputs of these commands:

stat /run/media/beta/DATA/Eric/CS_Working/CS-bodv-anp32a/J138/extract/BoDV_Host_1_23_26_9704_particles.mrc
stat -f /run/media/beta/DATA/Eric/CS_Working/CS-bodv-anp32a/J138/extract/BoDV_Host_1_23_26_9704_particles.mrc