Mesh prep error - "too many values to unpack"

[jcheung]

I’m getting this error that I can’t resolve when I try to define a custom mesh using the mesh prep module. Attached are screenshots showing the error and the segmentation from ChimeraX. The pink, red, gray, and green domains are all connected to the blue domain which I want to keep rigid. No matter how I define the segmentation connection topology,

in efforts to allow some of these domains to move independent of each other, I get this error.

Someone else reported this same error in the mesh prep module as well and there was no solution. Is this a bug in the module or is there something I’m doing wrong?

[wtempel]

@jcheung Did you observe this error in CryoSPARC v4.6.2?

[jcheung]

Yes, this is the version we have installed on our cluster.

[wtempel]

Thanks @jcheung Please can you post the output of this command (after replacing P99, J199 with the failed job’s project and job IDs):

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

[jcheung]

cryosparcuser@cryosparc5:~/cryosparc_master/bin$ ./cryosparcm cli “get_job(‘P313’, ‘J691’, ‘job_type’, ‘version’, ‘params_spec’, ‘input_slot_groups’, ‘errors_run’)”
{‘_id’: ‘677e6ffd9fbe42379d929454’, ‘errors_run’: , ‘input_slot_groups’: [{‘connections’: [{‘group_name’: ‘particles’, ‘job_uid’: ‘J689’, ‘slots’: [{‘group_name’: ‘particles’, ‘job_uid’: ‘J689’, ‘result_name’: ‘blob’, ‘result_type’: ‘particle.blob’, ‘slot_name’: ‘blob’, ‘version’: ‘F’}, {‘group_name’: ‘particles’, ‘job_uid’: ‘J689’, ‘result_name’: ‘ctf’, ‘result_type’: ‘particle.ctf’, ‘slot_name’: ‘ctf’, ‘version’: ‘F’}, {‘group_name’: ‘particles’, ‘job_uid’: ‘J689’, ‘result_name’: ‘alignments3D’, ‘result_type’: ‘particle.alignments3D’, ‘slot_name’: ‘alignments3D’, ‘version’: ‘F’}, {‘group_name’: ‘particles’, ‘job_uid’: ‘J689’, ‘result_name’: ‘alignments2D’, ‘result_type’: ‘particle.alignments2D’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘particles’, ‘job_uid’: ‘J689’, ‘result_name’: ‘pick_stats’, ‘result_type’: ‘particle.pick_stats’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘particles’, ‘job_uid’: ‘J689’, ‘result_name’: ‘location’, ‘result_type’: ‘particle.location’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘particles’, ‘job_uid’: ‘J689’, ‘result_name’: ‘ml_properties’, ‘result_type’: ‘particle.ml_properties’, ‘slot_name’: None, ‘version’: ‘F’}]}], ‘count_max’: inf, ‘count_min’: 1, ‘description’: ‘Particle stacks to use. Multiple stacks will be concatenated.’, ‘name’: ‘particles’, ‘repeat_allowed’: False, ‘slots’: [{‘description’: ‘’, ‘name’: ‘blob’, ‘optional’: False, ‘title’: ‘Particle data blobs’, ‘type’: ‘particle.blob’}, {‘description’: ‘’, ‘name’: ‘ctf’, ‘optional’: False, ‘title’: ‘Particle ctf parameters’, ‘type’: ‘particle.ctf’}, {‘description’: ‘’, ‘name’: ‘alignments3D’, ‘optional’: True, ‘title’: ‘Computed alignments (optional – only used to passthrough half set splits.)’, ‘type’: ‘particle.alignments3D’}, {‘description’: ‘’, ‘name’: ‘filament’, ‘optional’: True, ‘title’: ‘Particle filament info’, ‘type’: ‘particle.filament’}], ‘title’: ‘Particle stacks’, ‘type’: ‘particle’}], ‘job_type’: ‘homo_abinit’, ‘params_spec’: {‘abinit_K’: {‘value’: 2}, ‘abinit_class_anneal_beta’: {‘value’: 0.3}, ‘abinit_init_res’: {‘value’: 15}, ‘abinit_max_res’: {‘value’: 7}, ‘abinit_minisize’: {‘value’: 4000}, ‘abinit_minisize_init’: {‘value’: 3000}}, ‘project_uid’: ‘P313’, ‘uid’: ‘J691’, ‘version’: ‘v4.6.2’}

[wtempel]

@jcheung

‘job_type’: ‘homo_abinit’

Job P313.J691 does not seem to be a Mesh Prep job. Please can you double-check the IDs.

[jcheung]

Sorry about that. I have the correct IDs here:

cryosparcuser@cryosparc5:~/cryosparc_master/bin$ cryosparcm cli “get_job(‘P313’, ‘J673’, ‘job_type’, ‘version’,‘params_spec’, ‘input_slot_groups’, ‘errors_run’)”
{‘_id’: ‘677b6b219fbe42379d27d646’, ‘errors_run’: , ‘input_slot_groups’: [{‘connections’: [{‘group_name’: ‘particles_class_0’, ‘job_uid’: ‘J671’, ‘slots’: [{‘group_name’: ‘particles_class_0’, ‘job_uid’: ‘J671’, ‘result_name’: ‘blob’, ‘result_type’: ‘particle.blob’, ‘slot_name’: ‘blob’, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_0’, ‘job_uid’: ‘J671’, ‘result_name’: ‘ctf’, ‘result_type’: ‘particle.ctf’, ‘slot_name’: ‘ctf’, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_0’, ‘job_uid’: ‘J671’, ‘result_name’: ‘alignments3D’, ‘result_type’: ‘particle.alignments3D’, ‘slot_name’: ‘alignments3D’, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_0’, ‘job_uid’: ‘J671’, ‘result_name’: ‘alignments2D’, ‘result_type’: ‘particle.alignments2D’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_0’, ‘job_uid’: ‘J671’, ‘result_name’: ‘pick_stats’, ‘result_type’: ‘particle.pick_stats’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_0’, ‘job_uid’: ‘J671’, ‘result_name’: ‘location’, ‘result_type’: ‘particle.location’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_0’, ‘job_uid’: ‘J671’, ‘result_name’: ‘ml_properties’, ‘result_type’: ‘particle.ml_properties’, ‘slot_name’: None, ‘version’: ‘F’}]}, {‘group_name’: ‘particles_class_1’, ‘job_uid’: ‘J671’, ‘slots’: [{‘group_name’: ‘particles_class_1’, ‘job_uid’: ‘J671’, ‘result_name’: ‘blob’, ‘result_type’: ‘particle.blob’, ‘slot_name’: ‘blob’, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_1’, ‘job_uid’: ‘J671’, ‘result_name’: ‘ctf’, ‘result_type’: ‘particle.ctf’, ‘slot_name’: ‘ctf’, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_1’, ‘job_uid’: ‘J671’, ‘result_name’: ‘alignments3D’, ‘result_type’: ‘particle.alignments3D’, ‘slot_name’: ‘alignments3D’, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_1’, ‘job_uid’: ‘J671’, ‘result_name’: ‘alignments2D’, ‘result_type’: ‘particle.alignments2D’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_1’, ‘job_uid’: ‘J671’, ‘result_name’: ‘pick_stats’, ‘result_type’: ‘particle.pick_stats’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_1’, ‘job_uid’: ‘J671’, ‘result_name’: ‘location’, ‘result_type’: ‘particle.location’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘particles_class_1’, ‘job_uid’: ‘J671’, ‘result_name’: ‘ml_properties’, ‘result_type’: ‘particle.ml_properties’, ‘slot_name’: None, ‘version’: ‘F’}]}], ‘count_max’: inf, ‘count_min’: 1, ‘description’: ‘Particle stacks to use. Multiple stacks will be concatenated.’, ‘name’: ‘particles’, ‘repeat_allowed’: False, ‘slots’: [{‘description’: ‘’, ‘name’: ‘blob’, ‘optional’: False, ‘title’: ‘Particle data blobs’, ‘type’: ‘particle.blob’}, {‘description’: ‘’, ‘name’: ‘ctf’, ‘optional’: False, ‘title’: ‘Particle ctf parameters’, ‘type’: ‘particle.ctf’}, {‘description’: ‘’, ‘name’: ‘alignments3D’, ‘optional’: True, ‘title’: ‘Computed alignments (optional – only used to passthrough half set splits.)’, ‘type’: ‘particle.alignments3D’}, {‘description’: ‘’, ‘name’: ‘filament’, ‘optional’: True, ‘title’: ‘Particle filament info’, ‘type’: ‘particle.filament’}], ‘title’: ‘Particle stacks’, ‘type’: ‘particle’}], ‘job_type’: ‘homo_abinit’, ‘params_spec’: {‘abinit_K’: {‘value’: 2}, ‘abinit_class_anneal_beta’: {‘value’: 0.1}, ‘abinit_init_res’: {‘value’: 20}, ‘abinit_max_res’: {‘value’: 12}, ‘abinit_minisize’: {‘value’: 4000}, ‘abinit_minisize_init’: {‘value’: 1000}, ‘compute_use_ssd’: {‘value’: False}}, ‘project_uid’: ‘P313’, ‘uid’: ‘J673’, ‘version’: ‘v4.6.2’}

[jpellman]

Hi @wtempel ,

I think this might be the output that we want (J1673 instead of J673):

cryosparcuser@cryosparc5:~/cryosparc_master/bin$ cryosparcm cli “get_job(‘P313’, ‘J1673’, ‘job_type’, ‘version’,‘params_spec’, ‘input_slot_groups’, ‘errors_run’)”
{‘_id’: ‘67bb7237305c76615711fe44’, ‘errors_run’: [{‘message’: ‘too many values to unpack (expected 2)’, ‘warning’: False}], ‘input_slot_groups’: [{‘connections’: [{‘group_name’: ‘volume’, ‘job_uid’: ‘J1646’, ‘slots’: [{‘group_name’: ‘volume’, ‘job_uid’: ‘J1646’, ‘result_name’: ‘map’, ‘result_type’: ‘volume.blob’, ‘slot_name’: ‘map’, ‘version’: ‘F’}]}], ‘count_max’: 1, ‘count_min’: 1, ‘description’: ‘’, ‘name’: ‘volume’, ‘repeat_allowed’: False, ‘slots’: [{‘description’: ‘’, ‘name’: ‘map’, ‘optional’: False, ‘title’: ‘Consensus volume raw data’, ‘type’: ‘volume.blob’}], ‘title’: ‘Consensus volume’, ‘type’: ‘volume’}, {‘connections’: , ‘count_max’: 1, ‘count_min’: 0, ‘description’: ‘’, ‘name’: ‘mask’, ‘repeat_allowed’: False, ‘slots’: [{‘description’: ‘’, ‘name’: ‘mask’, ‘optional’: False, ‘title’: ‘Solvent mask’, ‘type’: ‘volume.blob’}], ‘title’: ‘Solvent mask’, ‘type’: ‘mask’}], ‘job_type’: ‘flex_meshprep’, ‘params_spec’: {‘mask_dilate_A’: {‘value’: 3}, ‘mask_in_threshold_level’: {‘value’: 0.25}, ‘mask_pad_A’: {‘value’: 6}, ‘tetra_rigid_list’: {‘value’: ‘956’}, ‘tetra_segments_fuse_list’: {‘value’: ‘956>1027>1024,956>1025>1026’}, ‘tetra_segments_path’: {‘value’: ‘/h1/jcheung/cryosparc/CS-hache-colq/uploads/J1647_map_250223_140624.seg’}}, ‘project_uid’: ‘P313’, ‘uid’: ‘J1673’, ‘version’: ‘v4.6.2’}

[wtempel]

Thanks @jcheung @jpellman. The definition of Segment Connections may be incorrect. If I interpret the intent correctly, you may want to instead try
956>1027,956>1025,1027>1024,1025>1026.

and let us know if that works.

[jcheung]

Yes this works just fine now. It wasn’t clear that the connections had to be strictly input in a pairwise manner.