Extract Task Error: particles.location Slot Must Be Connected

Particle Picking
1

Hi everyone,

I am encountering an issue with the extract task in CryoSPARC. Here’s a summary of the problem and my setup:

I have completed the local Refinement task and am now attempting to re-run the extract task with a larger box size to improve the particle extraction.

When I run the extract task, I receive the following error:

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What I’ve Tried:

  • Verified that all input connections are correct and properly set up.
  • Checked the particle location files to ensure they are correctly referenced.
    Could someone help me understand why this error is occurring and how I can resolve it? Specifically, I need guidance on ensuring that the particles.location slot is correctly connected and configured for the extract task.
2

@zhe Please can you post the expanded Particles section under the Inputs and Parameters tab. On recent CryoSPARC versions, you may have to check the Show slots option

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3

Thank you for your assistance.

I have attached three images as requested:

  1. First Image: Shows the “Show slots” view for the extract task with Task ID J617.
  2. Second Image: Another view of the “Show slots” for the same task.
  3. Third Image: Displays the source of the particles, which are from the local refine task with Task ID J530.

Please let me know if you need any further information or if there are additional steps I should take.

Thank you again for your help!

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4

Thanks @zhe for posting the screenshots. Can you identify an ancestor (parent, grandparent, etc.) job of J530 whose particles output has a location slot?

5

@wtempel, I am running version 4.6.0 and having the same issue. I had Run a 2D Classification job on a particular particle stack (template picks), then Select 2D from that job, then cleaned up the stack with iterative heterogeneous refinements against junk classes and a real class. Now I am trying to combine this stack with another particle stack (blob picks) and run Remove Duplicates. However, I now see that the particle locations somehow did not get connected or output in my Select 2D job for the template picks. Is there a way that I can re-connect the particle locations for my template picks now that the stack is much smaller than the original stack from Select 2D?

6

Hi @Cameron,

I’m sorry for the delayed response! Its possible that the particle.locations were dropped as an output somewhere in your processing pipeline. It might be worth looking into where in the pipeline that this occrued. To get around this, as you mention, you can connect an upstream particles.location output that contains the particles in the stack you wish to Remove Duplicates on, even if the particles.location contains particles that are not in the current particle stack.

All the best,
Kye