Remove duplicated particles -Error message

[abhipsa]

Hello
I’m encountering an issue while attempting to execute a ‘Remove Duplicate Particles’ job in CryoSPARC version 3.3.2.
The screenshots for both the error message and the input parameters are attached here.
The input particles used in this job were derived from a non-uniform refinement process, which, in turn, originated from particles ‘imported’ after performing Topaz picking in a different CryoSPARC account, and from a different IP address. Could that be a reason for the error message?

I would greatly appreciate any assistance in resolving this issue. Thank you for your help!

-Abhipsa

[CryoEM2]

I think those are particle picks, but have not been extracted? should work if you supply micrographs, or run particle extraction.

[wtempel]

@abhipsa Were you able to overcome this problem? If not, please can you

1. Paste the text, instead of the a screenshot, of the error message, to facilitate forum searches
2. Post a screenshot of the expanded particles input, so we may see what metadata were associated with the particles

[abhipsa]

Hi @wtempel Not yet.

1. Sure, The error message is below:
   License is valid.

Running job on master node

[CPU: 81.0 MB] Project P37 Job J92 Started

[CPU: 81.0 MB] Master running v3.3.2, worker running v3.3.2

[CPU: 81.5 MB] Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 52, in cryosparc_compute.run.main
File “/data1/cryosparc_user/cryosparc_excelsior/v3/cryosparc_master/cryosparc_compute/jobs/runcommon.py”, line 845, 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.

2. Apologies, but not sure where can I get the ‘expanded’ particles input from.

Nevertheless, I managed to execute the ‘Remove Duplicate Particles’ job within the CryoSPARC account that I used for Topaz picking (mentioned in my first message), leveraging access to micrographs associated with that specific account. So, I believe that the issues encountered were related to input parameters and different cryosparc accounts.

[wtempel]

@abhipsa

not sure where can I get the ‘expanded’ particles input from.

In pre-v4 CryoSPARC, you can expand inputs under the Inputs and Parameters tab:
non-expanded:

expanded:

@abhipsa

Nevertheless, I managed to execute the ‘Remove Duplicate Particles’ job within the CryoSPARC account that I used for Topaz picking (mentioned in my first message), leveraging access to micrographs associated with that specific account.

You may want to investigate whether the particle export-import workflow you mentioned

@abhipsa

input particles used in this job were derived from a non-uniform refinement process, which, in turn, originated from particles ‘imported’ after performing Topaz picking

somehow omitted or “lost” particles.location. How (job type, parameters) did you import those particles? You may want to also post screenshots of the Inputs and Parameters (expanded) and Outputs tabs of that import job.