Assertion error when running micrograph denoiser

Troubleshooting
1

Hello everyone,

I am trying to run the micrograph denoiser job on my curated exposures after doing motion correction and Patch CTF, but I get this error:

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 115, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/micrograph_analysis/run_denoise.py”, line 80, in cryosparc_master.cryosparc_compute.jobs.micrograph_analysis.run_denoise.run_train
AssertionError: Input micrographs must be background-subtracted. Use Patch Motion.

I followed the documentation:

Micrographs to be denoised, with background subtracted and CTF estimates available

I don’t understand why it is asking for patch motion even though it is already done in a previous step.

I would appreciate any help. Thanks in advance.

2

What version CS was the Patch Motion job run with? If it is al old (pre-4.5) job it won’t work - CS only started generating the required info in Patch Motion 4.5+

3

Thanks @olibclarke for pointing that out. Yes the Patch motion was indeed run with the older version of cryosparc. I will need to run a new Patch motion then.

4

Hi @Sarah!

I just want to make sure you saw the section of the guide on denoising data from existing patch motion jobs. This provides a workflow where you only need to re-process a couple hundred movies, not your entire dataset!

3 Likes
5

@rposert No I haven’t. I will check it out. Thank you for mentioning it!