RuntimeError: mrc_readmic (1) 481

Hi all,
I am having an issue with NU refinement. Firstly I imported my polishing file from relion using the Import Particle Stack job and then performed NU refinement, I got an error like this:

License is valid.

Launching job on lane default target localhost ...

Running job on master node hostname localhost

[CPU: 68.3 MB]   Project P12 Job J42 Started

[CPU: 68.3 MB]   Master running v3.3.2, worker running v3.3.2

[CPU: 68.6 MB]   Working in directory: /home/ZDQ/data2/cryosparc/P12/J42

[CPU: 68.6 MB]   Running on lane default

[CPU: 68.6 MB]   Resources allocated: 

[CPU: 68.6 MB]     Worker:  localhost

[CPU: 68.6 MB]     CPU   :  [0, 1, 2, 3]

[CPU: 68.6 MB]     GPU   :  [2]

[CPU: 68.6 MB]     RAM   :  [0, 1, 2]

[CPU: 68.8 MB]     SSD   :  True

[CPU: 68.8 MB]   --------------------------------------------------------------

[CPU: 68.8 MB]   Importing job module for job type nonuniform_refine_new...

[CPU: 232.9 MB]  Job ready to run

[CPU: 232.9 MB]  ***************************************************************
[CPU: 553.9 MB]  Traceback (most recent call last):
  File "cryosparc_worker/cryosparc_compute/", line 85, in
  File "cryosparc_worker/cryosparc_compute/jobs/refine/", line 114, in
  File "/home/ZDQ/Documents/cryosparc_worker/cryosparc_compute/", line 58, in init
    assert n.all(['blob/shape'][:,0] == self.N_input), "All particles must have the same box size."
AssertionError: All particles must have the same box size.

So I tried to extract my particles in pixel size of 0.93 in relion and then imported particles to cryosparc. When I performed NU refinement again, it came up that:

[CPU: 1.78 GB]   Traceback (most recent call last):
  File "/home/ZDQ/Documents/cryosparc_worker/cryosparc_compute/jobs/", line 1844, in run_with_except_hook
    run_old(*args, **kw)
  File "cryosparc_worker/cryosparc_compute/engine/", line 131, in
  File "cryosparc_worker/cryosparc_compute/engine/", line 132, in
  File "cryosparc_worker/cryosparc_compute/engine/", line 1028, in
  File "cryosparc_worker/cryosparc_compute/engine/", line 87, in cryosparc_compute.engine.engine.EngineThread.load_image_data_gpu
  File "/home/ZDQ/Documents/cryosparc_worker/cryosparc_compute/", line 22, in get_original_real_data
    return self.blob.view().copy()
  File "/home/ZDQ/Documents/cryosparc_worker/cryosparc_compute/blobio/", line 127, in view
    return self.get()
  File "/home/ZDQ/Documents/cryosparc_worker/cryosparc_compute/blobio/", line 122, in get
    _, data, total_time = prefetch.synchronous_native_read(self.fname, idx_start =, idx_limit =
  File "cryosparc_worker/cryosparc_compute/blobio/", line 69, in cryosparc_compute.blobio.prefetch.synchronous_native_read
RuntimeError: mrc_readmic (1) 481
Please report this as a bug.: Invalid argument
[arguments] /data2/cryosparc/instance_localhost:39001/imports/home/ZDQ/data2/20230412_XM/Extract/job067/movies/FoilHole_12293355_Data_12234370_12234372_20230413_090351_EER.mrcs, 0, 0, 57, 58, 2, 40

I try to restart cyrosparc now but keep getting this error. I don’t know what is happening and how to fix it?
My cryosparc version is v3.3.2
Any help is appreciated.

Hi @simone97 ,

I’d recommend upgrading to the latest CryoSPARC version, and seeing if the issue persists. There have been several fixes to our I/O code since then.