Particle subtraction failure

issue_recorded

#1

Hi,
I’ve started using cryosparc very recently and encounter an issue with the Particle Subtraction job. I use the version v2.12.4 of cryosparc and I basically followed the protocol described in the case study: Yeast U4/U6.U5 tri-snRNP. I payed extra care to check the mask boxes when needed (import masks and volume mask jobs) and kept the radius of reference window consistent with the one used in the refinement job.
The error message is as following:

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/local_refine/run_psub.py”, line 143, in cryosparc2_compute.jobs.local_refine.run_psub.run_particle_subtract
File “cryosparc2_compute/sigproc.py”, line 954, in compute_all_fscs
mask_in_real = initmask * (rMA + rMB)
ValueError: operands could not be broadcast together with shapes (200,200,200) (400,400,400)

Do you have an idea of what could the source of the problem? While waiting for you suggestion I going to redesign my masks and keep on trying…

Thanks


#2

Hi @laurie,

Thanks for reporting.
The error does indicate that the mask that you’ve used is stored in a volume with a different box size (200) than the volume that you are using for subtraction (400).
Can you try using the volume tools job to rescale the volume to the same size as the refinement map?
Let us know if that works!


#3

Hi @apunjani,

the refinement map I provide is supposed to be in a 200 voxel box, that’s the size I set up in the refinement job. The mask I create has the right dimension (200). So why the box of the refinement map is then doubled in the particle subtraction job?
I tried to resample the mask in the volume tool, the resulting mask as a lot of noise/dust and does not look like my mask anymore. I have anyway submitted this resampled mask to the particle subtraction job and obtained the same error message as previously except that it pops up right away the line"Pixel Size is 2.120" instead of after the later line “Scaling factor is 1.501”.

New error message:
Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/local_refine/run_psub.py”, line 85, in cryosparc2_compute.jobs.local_refine.run_psub.run_particle_subtract
ValueError: operands could not be broadcast together with shapes (200,200,200) (400,400,400)


#4

Also the same issue pops up when I try to run a local refinement job.


#5

@laurie thanks for reporting this also - given the steps you’ve taken we’re marking this as an issue that we are trying to reproduce here so it can be fixed.
Thanks!