Extract from micrographs shows neither error nor output

Dear all,

I recently had an issue with one extraction job and was wondering if someone could help.

I did process two of my datasets until ab-initio reconstruction and wanted to merge the datasets. But because of a mistake in the pixel size of one of those datasets it was impossible. I started reprocessing the dataset (import, motion correction and CTF estimation) with the correct pixel size. And here comes my problem. I want to extract only the particles from my last round of 2D classification (saving a lot of time and computational resources). My extraction job does run and finish (marked completed, no errors) but doesn’t display any output . Does anyone know what could be the issue?

Thank you in advance for your help.


Hi @Diane,

Thanks for posting. If I understand correctly, you would like to extract the particles using their original locations that were determined from the previous workflow, from the newly motion-corrected CTF-estimated movies. To do so, you can create a new ‘Extract from Micrographs’ job, and connect:

  • the ‘exposures’ output from your new CTF estimation job, and
  • the ‘particles’ output from your old 2D classification job

Can you please confirm this was the workflow used, and please provide any screenshots that might help us diagnose the missing outputs issue? Thanks!

Yes this is correct, it is the path I used.
On my console I also see that the errors file is empty (job.log.err).

Hi @Diane,
It looks like the particles are not actually being extracted/written to disk. Can you please post the job log?
You can get it from the command line interface:
cryosparcm joblog PX JX

I think you are correct the particles are not extracted. Nothing happens.

Hi @Diane,
Do you mind providing a screenshot of the Inputs and Parameters tab for this job?

Sure. No problem. I only used default parameters.

Hi @Diane, I’m sorry I should have been more clear, I am interested to see the low-level inputs of the J392.micrographs and J360.particles input, can you please open the dropdowns and then paste another screenshot? This is definitely a strange issue that we haven’t encountered before so I apologize for the lengthy troubleshoot!

Sorry I didn’t understand your request. I hope this is what you need.
Thank you for taking care of it.

Hi @Diane,

Is it possible that the micrographs you’re trying to extract particles from don’t actually have any valid particle locations? I noticed you’re connecting inputs from two separate jobs, presumably at different parts from your workflow (are you trying to re-extract particles?). Can you make sure that the particles input matches up properly with the exposures input (i.e. make sure the locations of the particles you’re trying to extract actually came from the micrographs you’ve connected to the job)?