I am currently trying to do a 2D classification after doing particle extraction using a Topaz trained model. When I run the “2D classification” job, I get the following error:
[CPU: 90.5 MB] Traceback (most recent call last):
** File “cryosparc2_worker/cryosparc2_compute/run.py”, line 52, in cryosparc2_compute.run.main**
** File “cryosparc2_compute/jobs/runcommon.py”, line 823, 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: particles.ctf. Please connect all required inputs.
This is a dataset that I just imported from another workstation. Please let me know if additional info is required.
You probably are missing one step: ‘Extract from Micrographs’.
I recommend the following order of jobs: Topaz Extract >> Inspect particle picks (use the ‘Power threshold’ to define a good cutoff) >> Extract from Micrographs.
Oh I think I see: Your micrographs need to have CTF estimation before doing classification and alignment. Before Topaz Extract, do this: Import Micrographs >> Patch CTF >> Topaz Extract using Patch CTF micrographs.
Can you double-check that the micrographs used in both the ‘Topaz Extract’ and ‘Extract from micrographs’ jobs both came from the micrographs in the Patch CTF job? The error you are getting ’ particles.ctf. Please connect all required inputs’ is complaining that there is no CTF information with the particles/micrographs you used.
So this has been my workflow. After patch CTF, I connected the output (exposures) > input to" template based particle picker". Followed this with a “inspect particle picks” job. I then connected the output micrographs of “Inspect particle picks” to topaz train job. I used the same micrographs along with the trained topaz model to do a “topaz extract”. I then connected the outputs of topaz extract as inputs to “Extract from micrographs” and finally connected the output to “2d class”.
That workflow looks fine. It’s pretty much what I do, except instead of template picking I do Topaz Extract pre-trained model. Maybe the Cryosparc team can help you get to the bottom of this.
Can you take a few screenshots: The “Outputs” tab for each job in your workflow. We have a hunch that it’s possible the CTF result of the micrograph wasn’t passed to the Extract From Micrographs job, causing the particles to not also have the CTF result fields.
