Import WARP particles to Cryosparc

Import and Export
1

Hi

I did processing in WARP and would like to import the particle to Cryosparc for further processing. I am able to import the particles but I am unable to get the corresponding particle locations.

Cryosparc is failing at finding the corresponding file names. It crashes with the following error,

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 115, in cryosparc_master.cryosparc_compute.run.main
File “/media/raid/cryosparc/cryosparc_worker/cryosparc_compute/jobs/imports/run.py”, line 254, in run_import_particles
assert qname in inv_index_source, “Could not find match for %s” % qname
AssertionError: Could not find match for FoilHole_19875168_Data_19844374_19844376_20240222_022543_fractions_patch_aligned_doseweighted.mrc

I provided the micrographs from patch CTF job as source exposure and enabled - remove leading UID in input exposure file name.

Also how important are the particle locations for further processing (I assume they are quite important ) ?

Please suggest.

Thanks

Abhi

2

Please can you describe how you imported the particles and how you confirmed that the import was successful?
Please can you also post the output of the command

cryosparcm cli "get_job('P99', 'J199', 'version', 'job_type', 'params_spec', 'status', 'input_slot_groups')"

where you replace P99 , J199 with the failed job’s (whose Traceback you have already posted) project and job IDs, respectively.
If the failed job involved the input of a star file, please post the star files header and first two data lines.

3

Hi wtempel,

Thank you for the response. I see the particles in the import job and was able to classify them as well. Unfortunately I don’t have access to the cryosparc cmd line. I will check with the admin to see what I can do with providing the output of the command you sent.

I have a similar issue with importing crypto particles to cryosparc:

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Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 115, in cryosparc_master.cryosparc_compute.run.main
File “/media/raid/cryosparc/cryosparc_worker/cryosparc_compute/jobs/imports/run.py”, line 254, in run_import_particles
assert qname in inv_index_source, “Could not find match for %s” % qname
AssertionError: Could not find match for FoilHole_19875168_Data_19844374_19844376_20240222_022543_fractions_patch_aligned_doseweighted.mrc

I looked into the cryosparc.star file generated by Cryolo and also the source micrographs which I input and I can see the _022543 mrc. Not sure why cryosparc could not find

Attached is the input parameter list

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Please suggest

Thanks

Abhi

4

If you can, please post

  • the CryoSPARC version
  • header and the first two data lines from the the file specified for the Particle meta path parameter
  • Were Source Micrographs connected to the Import Particles job? If so, please post a screenshot of the expanded Inputs section under the Inputs and Parameters tab