AssertionError: Gain reference for EER must be 4096 x 4096

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/”, line 84, in
File “/raid-18/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/”, 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/”, 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

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

The dataset is from 10424.

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?

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:

Hope that helps!

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This was it. Thanks!

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