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.