Error from 2D classfication job following importing particle stack from Relion

2D Classification
1

Hello,

I have imported particle.star job from Relion into cryopsarc however following inputting that job into 2D classification job I get the following error:

[CPU: 2.25 GB] Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 85, in cryosparc_compute.run.main
File “cryosparc_worker/cryosparc_compute/jobs/class2D/run.py”, line 159, in cryosparc_compute.jobs.class2D.run.run_class_2D
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/particles.py”, line 32, in get_prepared_fspace_data
return fourier.resample_fspace(fourier.fft(self.get_prepared_real_data()), self.dataset.N)
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/particles.py”, line 27, in get_prepared_real_data
return (self.dataset.prepare_normalization_factor * self[‘blob/sign’]) * (self.dataset.prepare_real_window * (self.get_original_real_data()))
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/particles.py”, line 22, in get_original_real_data
return self.blob.view().copy()
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 127, in view
return self.get()
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 122, in get
_, data, total_time = prefetch.synchronous_native_read(self.fname, idx_start = self.page, idx_limit = self.page+1)
File “cryosparc_worker/cryosparc_compute/blobio/prefetch.py”, line 69, in cryosparc_compute.blobio.prefetch.synchronous_native_read
TypeError: sync_io(): incompatible function arguments. The following argument types are supported:
1. (arg0: str, arg1: int, arg2: int, arg3: int, arg4: int, arg5: int, arg6: int) → tuple

Invoked with: b’/home/cryosparc/cryosparc_cache/instance_host/imports/mnt/md0/SNestorow/raw4_EBIC/Extract/job008/Movies/FoilHole_23777566_Data_23771393_23771395_20231123_192739_fractions_motion_corrected.mrcs’, 0, 0, 4294967295, 4294967296, 2, 40

I am not sure what this error means to know how to go about correcting it - any help would be much appreciated!

Thanks

2

It’s having an issue finding or recognizing the location of particles. is it possible that your cryosparc location is different from where relion stores the data? can you try copying the extraction folder to your cryosparc location and then modifying the particles.star to refer to that new location? have you (or any of your colleagues) imported relion particles to cryosparc before, with this setup? might be good to mimic a process internal to your colleagues.

3

Hi, thank you for quick response! I have exported the ‘Extract’ relion job folder as this is from processing done at a facility to finish processing at home institute - I assume this means I need to edit the .star text file to the new location?

4

yes. global search and replace the path at the beginning of particles description in the star, directing to the new (cryosparc accessible) location of that folder.