AssertionError: Gain reference for EER must be 4096 x 4096

Troubleshooting
1

I am trying to import EER movies. I keep getting the “AssertionError: Gain reference for EER must be 4096 x 4096”. The only option to change is the EER upsampling factor which can be set 1,2 or 4. I get the same error no matter which value I choose.

License is valid.

Running job on master node

[CPU: 67.8 MB] Project P2 Job J24 Started

[CPU: 67.9 MB] Master running v3.2.0, worker running v3.2.0

[CPU: 67.9 MB] Running on lane Mortimer

[CPU: 67.9 MB] Resources allocated:

[CPU: 67.9 MB] Worker: vis-1.mortimer

[CPU: 67.9 MB] --------------------------------------------------------------

[CPU: 67.9 MB] Importing job module for job type import_movies…

[CPU: 205.9 MB] Job ready to run

[CPU: 205.9 MB] ***************************************************************

[CPU: 205.9 MB] Importing movies from /Data/tmalla/EM/archive/10309/data/Movies/*.eer

[CPU: 205.9 MB] Importing 3370 files

[CPU: 205.9 MB] Import paths were unique at level -1

[CPU: 205.9 MB] Importing 3371 files

[CPU: 205.9 MB] ‘Skip Header Check’ parameter enabled, checking first header only

[CPU: 206.4 MB] EER data imported with upsampling factor 2.00. Old pixel size: 0.4570 new pixel size 0.2285

[CPU: 206.4 MB] Reading headers of gain reference file /home/tmalla/Data/tmalla/EM/archive/10424/data/gainImage_8k_defMasked.mrc
[CPU: 206.4 MB] Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main
File “/raid-18/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py”, line 816, in run_import_movies_or_micrographs
gshapey, gshapex = read_gain_reference(gainref_abs_path, shape_only=True, data_format=data_format)
File “/raid-18/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py”, line 802, in read_gain_reference
assert gshapex == gshapey == 4096, “Gain reference for EER must be 4096 x 4096”
AssertionError: Gain reference for EER must be 4096 x 4096

2

@73km, are you processing an EMPIAR dataset? If so, which one?

3

The dataset is from 10424.

4

The program imports the movies if the gain reference file is not provided. Aside from EER fraction and upsampling factors, is there anything else that need to tweaked?

5

Hi @73km, EMPIAR-10424 includes a gain reference in an older file format from before the EER specification was finalized, so cryoSPARC does not implement support for it.

One of my colleagues re-generated the gain reference in the correct format. You can download it from following link and use it instead for your processing: https://drive.google.com/file/d/1kVOMJUqNRvP0uqQYNGZ8bzLX3VAJhRwC/view?usp=sharing

Hope that helps!

1 Like
6

This was it. Thanks!

1 Like