Error importing particles from RELION5

Import and Export
1

Apologies if this has already been posted but I wasn’t able to find anything recent. I’m having trouble importing particles from a RELION5 star file to cryosparc V4.6.0. I provided a star file for the metadata path and the path to my RELION project directory as the particle data path. The import job completes okay but I receive the following warnings and the metadata is not properly imported.

Warning: Parameter particle_blob_path was set, which overrides rlnImageName despite the latter being present in the input star file.

Parameter particle_blob_path was set and is a directory, so will be used as the search base for finding referenced data paths in the star file.

Warning: The input star file does not contain rlnVoltage, and parameter accel_kv was not set. Output will not contain CTF parameters for particles.

Warning: The input star file does not contain rlnSphericalAberration, and parameter cs_mm was not set. Output will not contain CTF parameters for particles.

Warning: No exposures were connected as inputs, so correspondences cannot be found, so output will not contain pick locations for particles.

As far as I can tell the star file format has not changed and the indicated CTF parameters are present in the input.

Fields loaded from star file:  ['rlnOpticsGroup', 'rlnOpticsGroupName', 'rlnAmplitudeContrast_x', 'rlnSphericalAberration_x', 'rlnVoltage_x', 'rlnImagePixelSize', 'rlnImageSize', 'rlnImageDimensionality', 'rlnCtfDataAreCtfPremultiplied', 'rlnMicrographName', 'rlnCoordinateX', 'rlnCoordinateY', 'rlnImageName', 'rlnDefocusU', 'rlnDefocusV', 'rlnDefocusAngle', 'rlnPhaseShift', 'rlnVoltage_y', 'rlnSphericalAberration_y', 'rlnAmplitudeContrast_y', 'rlnMagnification', 'rlnDetectorPixelSize', 'rlnAngleRot', 'rlnAngleTilt', 'rlnAnglePsi', 'rlnOriginXAngst', 'rlnOriginYAngst', 'rlnRandomSubset', 'rlnClassNumber', 'rlnNormCorrection', 'rlnLogLikeliContribution', 'rlnMaxValueProbDistribution', 'rlnNrOfSignificantSamples', 'rlnGroupName', 'rlnGroupNumber']

Star file optics table:

# version 50001

data_optics

loop_ 
_rlnOpticsGroup #1 
_rlnOpticsGroupName #2 
_rlnAmplitudeContrast #3 
_rlnSphericalAberration #4 
_rlnVoltage #5 
_rlnImagePixelSize #6 
_rlnImageSize #7 
_rlnImageDimensionality #8 
_rlnCtfDataAreCtfPremultiplied #9 
           1 opticsGroup1     0.070000     2.700000   300.000000     2.089688          128            2            0
2

@RyanFeathers Please can you post the output of the command

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

where you replace P99, J199 with the import job’s project and job ID’s, respectively.

3

Here’s the requested output with the hostname and data paths edited.

 cryosparcm cli "get_job('P653', 'J1', 'job_type', 'version', 'instance_information', 'status',  'params_spec', 'errors_run')"
{'_id': '67210735a811e8ef6d9883f9', 'errors_run': [], 'instance_information': {'available_memory': '162.50GB', 'cpu_model': 'Intel(R) Xeon(R) Gold 6142 CPU @ 2.60GHz', 'ofd_hard_limit': 5120, 'ofd_soft_limit': 5120, 'physical_cores': 32, 'platform_architecture': 'x86_64', 'platform_node': 'HOSTNAME', 'platform_release': '4.18.0-553.22.1.el8_10.x86_64', 'platform_version': '#1 SMP Wed Sep 11 18:02:00 EDT 2024', 'total_memory': '186.88GB', 'used_memory': '19.68GB'}, 'job_type': 'import_particles', 'params_spec': {'alignments3D_exists': {'value': True}, 'blob_exists': {'value': True}, 'enable_validation': {'value': True}, 'particle_blob_path': {'value': 'PATH_TO_RELION_PROJECT'}, 'particle_meta_path': {'value': 'PATH_TO_RELION_PROJECT/Extract/job012/particles.star'}}, 'project_uid': 'P653', 'status': 'completed', 'uid': 'J1', 'version': 'v4.6.0'}
4

@RyanFeathers Please can you email the file job012/particles.star to us?

5

Emailed, please let me know if you aren’t able to download the file

6

Thanks. Downloaded successfully.

7

Hi @RyanFeathers, sorry for the delay. We found an issue when we import a STAR file which has optics data in both the optics and data tables. While we work to fix this, you can delete the optics table of the STAR file and manually enter the relevant information (voltage, Cs, etc.) and it should import smoothly!

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