Error with linked inputs during local motion correction

solved

#1

I am following along the steps in the T20S Tutorial with my own data set and have encountered an issue when attempting to carry out local motion correction following particle picking. The error encountered is below:

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 49, in cryosparc2_compute.run.main
File “cryosparc2_compute/jobs/runcommon.py”, line 325, in check_default_inputs
assert False, 'Non-optional inputs from the following input groups and their slots are not connected: ’ + missing_inputs + ‘. Please connect all required inputs.’
AssertionError: Non-optional inputs from the following input groups and their slots are not connected: movies.background_blob. Please connect all required inputs.

If I understand correctly, it’s looking for a file that should be connected to this job called movies.background_blob, but in looking through the outputs from importing the movies up to this step, I can’t seem to see any files that have that name.

Has anybody else encountered this issue? I am very much a beginner with cryo-EM data processing and it’s entirely possible that I’m missing something obvious.

Cheers,
SW


#2

Update: It appears that the issue was probably trying to use MotionCor2 (BETA) rather than the Full-frame motion correction, as I am seeing a .background_blob file in my output now.


#3

Hi @seandworkman,

You’re on the right track! Theres no need to execute a local motion estimate of particles on micrographs that have already been aligned by MotionCor2. Micrographs that come out of MotionCor2 are full-frame and locally (by patches) aligned- you can put those micrographs directly into an “extract from micrographs” job to get your particles and go to the next step (usually a 2D class since these particle picks are probably from the template picker). Let me know if you have any more questions and all the best.


#4

Okay great! I didn’t realize that MotionCor2 was doing local motion correction for me as well as full-frame. Like I said, very much a beginner. Thanks so much for clarifying! :slight_smile: