Remove duplicates job is failing on missing inputs (v3.3.2+220824)

Utilities
1

Hello,

I have been processing this data for several months and decided to go back to a particular stack to do some quantification. I tried to run a remove duplicates job and received the following error:

Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 52, in cryosparc_compute.run.main
  File "/admin/opt/common/cryosparc3.1/cryosparc_master/cryosparc_compute/jobs/runcommon.py", line 838, 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.location. Please connect all required inputs.

I tried this both with and without micrographs provided as inputs (providing pixel size instead). Thinking it may have been the particular particle stack, I went to another stack and tried the same thing to no avail. Am I missing something here?

Best regards,
Navid

2

As another sanity check, I cloned and re-ran the local refinement, fed those outputs into remove duplicates, and it fails again.

3

Please can you post a screenshot of the expanded inputs from the Inputs and Parameters tab?

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4

Here you go, I see the location is missing - how can I remedy this?

Screen Shot 2022-11-14 at 5.53.18 PM
Screen Shot 2022-11-14 at 5.53.18 PM530×828 51.4 KB

5

What type of job was J3361? Maybe if you trace back, you can see where the particle location disappeared, and then replace it here using the low level results interface?

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6

J3361 is a Remove Duplicates job. I’m looking for particle location meta data in the low level jobs and only Extract or Particle Sets jobs, as far as I can tell, contain this link. Strangely, Import jobs do not. This particle stack was imported from a Relion Polish job. Also, I can successfully run a Local Refinement on this stack prior to the Remove Duplicates job. I’m a little stumped.

7

Hi Navid, if you import particles from relion without associating with a set of micrographs, the locations will be lost. Maybe that is what happened?

It is not surprising that you can run Local Refinement on these particles - the particle locations are not needed for this, only the relative offsets.

1 Like
8

It turns out this was the result of some corrupted data. Re-ran the entire branch and recovered.

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