@spunjani Thank you for your reply.
I did this and ran the particle input job. It completed and the # of particles were correct but there were a bunch of warnings (see below).
I used the particles from above and tried to start a local refinement job with volume/mask from an earlier cryosparc job and got an error - it seems some essential information is missing in the run_data.star and I’m not sure how to put it back. Any suggestions?
Warnings during import particle job:
[CPU: 551.1 MB] Loaded star file with 684804 items
[CPU: 551.1 MB] Fields loaded from star file: ['rlnVoltage', 'rlnSphericalAberration', 'rlnAmplitudeContrast', 'rlnOpticsGroup', 'rlnImageSize', 'rlnImagePixelSize', 'rlnImageDimensionality', 'rlnImageName', 'rlnAngleRot', 'rlnAngleTilt', 'rlnAnglePsi', 'rlnOriginXAngst', 'rlnOriginYAngst', 'rlnDefocusU', 'rlnDefocusV', 'rlnDefocusAngle', 'rlnPhaseShift', 'rlnCtfBfactor', 'rlnRandomSubset', 'rlnClassNumber', 'rlnGroupNumber', 'rlnNormCorrection', 'rlnLogLikeliContribution', 'rlnMaxValueProbDistribution', 'rlnNrOfSignificantSamples']
[CPU: 551.1 MB] **Warning**: The input star file does not contain rlnDetectorPixelSize and rlnMagnification, and parameter psize_A was not set. Output will not contain data for particles.
[CPU: 551.1 MB] --------------------------------------------------------------
[CPU: 551.1 MB] Compiling CTF information...
[CPU: 551.3 MB] **Warning**: The input star file does not contain rlnCoordinateX and rlnCoordinateY and rlnMicrographName. Output will not contain pick locations for particles.
[CPU: 551.3 MB] **Warning:** Output will not contain particle orientations since parameter 'psize_A' was not set.
[CPU: 551.3 MB] --------------------------------------------------------------
[CPU: 551.3 MB] Particle information has now been imported for 684804 particles, creating outputs...
[CPU: 575.8 MB] --------------------------------------------------------------
[CPU: 575.8 MB] Loaded 684804 particles.
[CPU: 575.8 MB] Common fields:
[CPU: 575.8 MB] ctf/accel_kv : {300.0}
[CPU: 575.8 MB] ctf/cs_mm : {2.7}
[CPU: 575.8 MB] ctf/amp_contrast : {0.1}
[CPU: 575.8 MB] ctf/exp_group_id : {1, 2}
[CPU: 209.5 MB] --------------------------------------------------------------
[CPU: 209.5 MB] Compiling job outputs...
[CPU: 209.5 MB] Updating job size...
[CPU: 209.5 MB] Exporting job and creating csg files...
Error when I tried to start local refinement from the imported particles:
[CPU: 82.1 MB] Traceback (most recent call last):
File "cryosparc_worker/cryosparc_compute/run.py", line 52, in cryosparc_compute.run.main
File "/home/cryosparc_user/software/cryosparc/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py", line 847, in check_default_inputs
assert False, 'Non-optional inputs from the following input groups and their slots are not connected: ' + missing_inputs + '. Please connect all required inputs.'
AssertionError: **Non-optional inputs from the following input groups and their slots are not connected**: particles.blob, particles.alignments3D. Please connect all required inputs.
