Import particle metadata from star file (AssertionError: The following outputs were expected but not produced: pick_stats)

Import and Export
1

The star file contain only micrograph and coordinateX/Y. When importing particle metadata in cryosparc v4.5.3, error happens (see below).
[CPU: 318.7 MB Avail: 240.37 GB]

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 115, in cryosparc_master.cryosparc_compute.run.main
File “/data/sw/cryosparc/cryosparc_worker/cryosparc_compute/jobs/imports/run.py”, line 465, in run_import_particles
assert len(validation_errors) == 0, "The following outputs were expected but not produced: " + ", ".join(validation_errors)
AssertionError: The following outputs were expected but not produced: pick_stats

2

@jianhaoc Please can you post:

  1. Details about the origin of the star file
  2. The header and first few records of your star file
  3. Output of the following command
    cryosparcm cli "get_job('P99', 'J199', 'job_type', 'params_spec')"
    where you replace P99, J199 with the failed job’s project and job IDs, respectively
3

data_

loop_
_rlnMicrographName #1
_rlnCoordinateX #2
_rlnCoordinateY #3
_rlnAutopickFigureOfMerit #4
20240626-g1f-slot2_119_019_X+1Y+1-6_sum.mrc 4991.041488647461 2493.562987804413 0.14819349348545074
20240626-g1f-slot2_139_029_X-1Y+1-2_sum.mrc 1407.9331398010254 447.5627439022064 0.05520161986351013
20240626-g1f-slot2_139_035_X-1Y+0-1_sum.mrc 4731.657371520996 3588.039931833744 0.010997476987540722
20240626-g1f-slot2_148_048_X-1Y-1-0_sum.mrc 4671.324577331543 3197.0232315659523 0.5968583822250366
20240626-g1f-slot2_159_054_X+0Y-1-6_sum.mrc 3263.998603820801 3324.7502439022064 0.04506153240799904
20240626-g1f-slot2_162_012_X+1Y+0-6_sum.mrc 5438.784828186035 3452.7448169589043 0.002797327935695648

$ cryosparcm cli “get_job(‘P1’, ‘J109’, ‘job_type’, ‘params_spec’)”
{‘_id’: ‘668da771b6f93e705ee1da3f’, ‘job_type’: ‘import_particles’, ‘params_spec’: {‘accel_kv’: {‘value’: 300}, ‘amp_contrast’: {‘value’: 0.1}, ‘cs_mm’: {‘value’: 2.7}, ‘e
nable_validation’: {‘value’: True}, ‘ignore_blob’: {‘value’: True}, ‘ignore_pose’: {‘value’: True}, ‘location_exists’: {‘value’: True}, ‘particle_meta_path’: {‘value’: ‘/d
ata/d/g1f-slot2-20240626/cryosparc.star’}, ‘psize_A’: {‘value’: 0.666}, ‘remove_leading_uid’: {‘value’: True}, ‘sign’: {‘val
ue’: ‘dark-on-light’}}, ‘project_uid’: ‘P1’, ‘uid’: ‘J109’}

4

Hi @jianhaoc,

Thanks for bearing with us. Could you try disabling the parameter entitled “Enable Strict Checking”, and re-running the job?

If that still produces errors, could you additionally remove the _rlnAutopickFigureOfMerit column from the input star file (along with the numerical data associated with that field), and then re-run the job?

Michael