Hello! I was running CryoSPARC on a computer that went out of service. All the data was copied to a new computer, and I loaded the old projects in the new computer’s CryoSPARC with the option “New Project > Attach Project”. I can see all the jobs that correspond to the old project in the new computer, I can download maps, etc. The issue is, when I try to run a new job with the particles that correspond to the old project, I get the following error: “AssertionError: Unsupported MRC datatype: 842346550”. It does not matter which kind of job I run, so far I only got the same error.
Is there any way for me to fix this without having to re-import the particles?
What versions of cryosparc is/was installed on the old and the new computer?
Okay that is funny actually. The particles from the old computer say v4.2.1 but I am pretty sure that the old computer never had cryoSPARC beyond 3.something. That being said, I get the same error even when I try to run jobs with particles that are from v3 from the old computer.
The new computer has v4.3.1
Welcome to the forum @MicaelaBS.
Please can you post:
- the Traceback from the screenshot as text
- a screenshot of the failed job’s Inputs under the Inputs and Parameters tab
- the job types of the jobs that occur in the Inputs section
- output of the command
where you substitutedcryosparcm cli "get_job('PX', 'JY', 'job_type', 'version', 'params_spec')"PX,JYwith the job’s actual project and job IDs
*Traceback:
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 95, in cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/var3D/run.py”, line 75, in cryosparc_compute.jobs.var3D.run.run
File “/home_local/cryosparc_admin/cryosparc_worker/cryosparc_compute/particles.py”, line 130, in read_blobs
dtypes[rel_path] = mrc.mrc_datatype_to_dtype(hdr[‘datatype’])
File “/home_local/cryosparc_admin/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 67, in mrc_datatype_to_dtype
assert False,‘Unsupported MRC datatype: {0}’.format(datatype)
AssertionError: Unsupported MRC datatype: 842346550
-
Input screenshot
-
The job I ran is a 3D variability, the input jobs are a mask and particles coming from a NU refinement (J632). This job had already ran without issues in the old pc, I re-imported the project, cloned the job and when I try to run it again it fails. All the jobs I ran fail with the same error, this 3D variability is just an example.
- Output of the command:
{'PID_main': 280273, 'PID_monitor': 280272, 'PID_workers': [], '_id': '657b2a5f4b5c61ce22af4033', 'bench': {}, 'children': [], 'cloned_from': 'J700', 'cluster_job_custom_vars': {}, 'cluster_job_id': None, 'cluster_job_monitor_event_id': None, 'cluster_job_monitor_last_run_at': None, 'cluster_job_monitor_retries': 0, 'cluster_job_status': None, 'cluster_job_status_code': None, 'cluster_job_submission_script': None, 'completed_at': None, 'completed_count': 0, 'created_at': 'Thu, 14 Dec 2023 16:16:31 GMT', 'created_by_job_uid': None, 'created_by_user_id': '61680b2a5c067dc0d32b61b5', 'deleted': False, 'description': 'Enter a description.', 'enable_bench': False, 'errors_build_inputs': {}, 'errors_build_params': {}, 'errors_run': [{'message': 'Unsupported MRC datatype: 842346550', 'warning': False}], 'experiment_worker_path': None, 'failed_at': 'Thu, 14 Dec 2023 16:17:44 GMT', 'generate_intermediate_results': False, 'heartbeat_at': 'Thu, 14 Dec 2023 16:17:41 GMT', 'input_slot_groups': [{'connections': [{'group_name': 'particles', 'job_uid': 'J632', 'slots': [{'group_name': 'particles', 'job_uid': 'J632', 'result_name': 'blob', 'result_type': 'particle.blob', 'slot_name': 'blob', 'version': 'F'}, {'group_name': 'particles', 'job_uid': 'J632', 'result_name': 'ctf', 'result_type': 'particle.ctf', 'slot_name': 'ctf', 'version': 'F'}, {'group_name': 'particles', 'job_uid': 'J632', 'result_name': 'alignments3D', 'result_type': 'particle.alignments3D', 'slot_name': 'alignments3D', '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': False, 'title': 'Particle alignments3D parameters', 'type': 'particle.alignments3D'}], 'title': 'Particle stacks', 'type': 'particle'}, {'connections': [{'group_name': 'mask', 'job_uid': 'J632', 'slots': [{'group_name': 'mask', 'job_uid': 'J632', 'result_name': 'mask_refine', 'result_type': 'volume.blob', 'slot_name': 'mask', 'version': 'F'}]}], 'count_max': 1, 'count_min': 1, 'description': '', 'name': 'mask', 'repeat_allowed': False, 'slots': [{'description': '', 'name': 'mask', 'optional': False, 'title': 'Mask raw data', 'type': 'volume.blob'}], 'title': 'Mask', 'type': 'mask'}], 'instance_information': {'CUDA_version': '11.8.0', 'available_memory': '114.87GB', 'cpu_model': 'Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz', 'gpu_info': [{'id': 0, 'mem': 8507949056, 'name': 'NVIDIA GeForce GTX 1080'}], 'ofd_hard_limit': 1048576, 'ofd_soft_limit': 1024, 'physical_cores': 8, 'platform_architecture': 'x86_64', 'platform_node': 'gpur1.srv-local.mpi-dortmund.mpg.de', 'platform_release': '6.2.0-37-generic', 'platform_version': '#38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2', 'total_memory': '125.63GB', 'used_memory': '9.25GB'}, 'interactive': False, 'interactive_hostname': 'gpur1.srv-local.mpi-dortmund.mpg.de', 'interactive_port': None, 'intermediate_results_size_bytes': 0, 'intermediate_results_size_last_updated': None, 'is_ancestor_of_final_result': False, 'is_experiment': False, 'is_final_result': False, 'job_dir': 'J718', 'job_dir_size': 0, 'job_dir_size_last_updated': None, 'job_sig': '94512977258255726484477671385656165160598061883257162626922990790643055333616901145274566117013067361071549316867894158574335357470712982914070126062532365089644266567898639073411963893824273331430384991602130024786979789770978620197118944439937692409012546304478622675547531936538031720673554029561670609174852700455366473918343596308172173216648413832242000496821275810577168676629586517518350656482302363439692478240209806370437928713637828989688721712454919731157880852160805962181779031257304046882218507955628910656881714367237344678352167672645943004283679562731980520360274948382839045420556398171983245225553523133436160905224552729358481777711674150902575622586637034546923188894982633676521192159451282226065745340131137876105700895010166400685931608197459614179428914555700836851811946678402022498262266063519689126699209116668560477574767808849620073982703749287740995289023814251050588135707323662757403350589238905637778462732440062210626648785700088580048338050567699460891774242435355073535007913794816811933949114783264643550014695478429644110987588316760535119866626485772692330991477881978752908132605471375035849440884873221329874391435384512661067165286025875568996425841544879720798372027254690310011805629901', 'job_type': 'var_3D', 'killed_at': None, 'last_accessed': {'accessed_at': 'Wed, 21 Feb 2024 09:16:36 GMT', 'name': 'm.boierosanders'}, 'last_exported': 'Thu, 14 Dec 2023 16:16:46 GMT', 'last_intermediate_data_cleared_amount': 0, 'last_intermediate_data_cleared_at': None, 'last_scheduled_at': None, 'last_updated': 'Wed, 21 Feb 2024 09:16:36 GMT', 'launched_at': 'Thu, 14 Dec 2023 16:17:25 GMT', 'no_check_inputs_ready': False, 'num_tokens': 1, 'output_group_images': {}, 'output_result_groups': [{'contains': [{'group_name': 'particles', 'name': 'components_mode_0', 'passthrough': False, 'type': 'particle.components', 'uid': 'J718-R1'}, {'group_name': 'particles', 'name': 'components_mode_1', 'passthrough': False, 'type': 'particle.components', 'uid': 'J718-R3'}, {'group_name': 'particles', 'name': 'components_mode_2', 'passthrough': False, 'type': 'particle.components', 'uid': 'J718-R5'}, {'group_name': 'particles', 'name': 'blob', 'passthrough': True, 'type': 'particle.blob', 'uid': 'J718-R7'}, {'group_name': 'particles', 'name': 'ctf', 'passthrough': True, 'type': 'particle.ctf', 'uid': 'J718-R8'}, {'group_name': 'particles', 'name': 'alignments3D', 'passthrough': True, 'type': 'particle.alignments3D', 'uid': 'J718-R9'}], 'description': 'All particles that were processed, including alignments', 'name': 'particles', 'num_items': 0, 'passthrough': 'particles', 'summary': {}, 'title': 'All particles', 'type': 'particle', 'uid': 'J718-G0'}, {'contains': [{'group_name': 'volume', 'name': 'map', 'passthrough': False, 'type': 'volume.blob', 'uid': 'J718-R0'}, {'group_name': 'volume', 'name': 'component_0', 'passthrough': False, 'type': 'volume.blob', 'uid': 'J718-R2'}, {'group_name': 'volume', 'name': 'component_1', 'passthrough': False, 'type': 'volume.blob', 'uid': 'J718-R4'}, {'group_name': 'volume', 'name': 'component_2', 'passthrough': False, 'type': 'volume.blob', 'uid': 'J718-R6'}], 'description': '', 'name': 'volume', 'num_items': 0, 'passthrough': False, 'summary': {}, 'title': '3D Variability volumes', 'type': 'volume', 'uid': 'J718-G1'}], 'output_results': [{'description': '', 'group_name': 'volume', 'metafiles': [], 'min_fields': [['path', 'O'], ['shape', '3u4'], ['psize_A', 'f4']], 'name': 'map', 'num_items': [], 'passthrough': False, 'title': 'Filtered consensus map', 'type': 'volume.blob', 'uid': 'J718-R0', 'versions': []}, {'description': '', 'group_name': 'particles', 'metafiles': [], 'min_fields': [['component', 'u4'], ['value', 'f4']], 'name': 'components_mode_0', 'num_items': [], 'passthrough': False, 'title': 'Components class 0', 'type': 'particle.components', 'uid': 'J718-R1', 'versions': []}, {'description': '', 'group_name': 'volume', 'metafiles': [], 'min_fields': [['path', 'O'], ['shape', '3u4'], ['psize_A', 'f4']], 'name': 'component_0', 'num_items': [], 'passthrough': False, 'title': 'Component data', 'type': 'volume.blob', 'uid': 'J718-R2', 'versions': []}, {'description': '', 'group_name': 'particles', 'metafiles': [], 'min_fields': [['component', 'u4'], ['value', 'f4']], 'name': 'components_mode_1', 'num_items': [], 'passthrough': False, 'title': 'Components class 1', 'type': 'particle.components', 'uid': 'J718-R3', 'versions': []}, {'description': '', 'group_name': 'volume', 'metafiles': [], 'min_fields': [['path', 'O'], ['shape', '3u4'], ['psize_A', 'f4']], 'name': 'component_1', 'num_items': [], 'passthrough': False, 'title': 'Component data', 'type': 'volume.blob', 'uid': 'J718-R4', 'versions': []}, {'description': '', 'group_name': 'particles', 'metafiles': [], 'min_fields': [['component', 'u4'], ['value', 'f4']], 'name': 'components_mode_2', 'num_items': [], 'passthrough': False, 'title': 'Components class 2', 'type': 'particle.components', 'uid': 'J718-R5', 'versions': []}, {'description': '', 'group_name': 'volume', 'metafiles': [], 'min_fields': [['path', 'O'], ['shape', '3u4'], ['psize_A', 'f4']], 'name': 'component_2', 'num_items': [], 'passthrough': False, 'title': 'Component data', 'type': 'volume.blob', 'uid': 'J718-R6', 'versions': []}, {'description': 'Passthrough from input particles.blob (slot_name)', 'group_name': 'particles', 'metafiles': [], 'min_fields': [['path', 'O'], ['idx', 'u4'], ['shape', '2u4'], ['psize_A', 'f4'], ['sign', 'f4'], ['import_sig', 'u8']], 'name': 'blob', 'num_items': [], 'passthrough': True, 'title': 'Passthrough blob', 'type': 'particle.blob', 'uid': 'J718-R7', 'versions': []}, {'description': 'Passthrough from input particles.ctf (slot_name)', 'group_name': 'particles', 'metafiles': [], 'min_fields': [['type', 'O'], ['exp_group_id', 'u4'], ['accel_kv', 'f4'], ['cs_mm', 'f4'], ['amp_contrast', 'f4'], ['df1_A', 'f4'], ['df2_A', 'f4'], ['df_angle_rad', 'f4'], ['phase_shift_rad', 'f4'], ['scale', 'f4'], ['scale_const', 'f4'], ['shift_A', '2f4'], ['tilt_A', '2f4'], ['trefoil_A', '2f4'], ['tetra_A', '4f4'], ['anisomag', '4f4'], ['bfactor', 'f4']], 'name': 'ctf', 'num_items': [], 'passthrough': True, 'title': 'Passthrough ctf', 'type': 'particle.ctf', 'uid': 'J718-R8', 'versions': []}, {'description': 'Passthrough from input particles.alignments3D (slot_name)', 'group_name': 'particles', 'metafiles': [], 'min_fields': [['split', 'u4'], ['shift', '2f4'], ['pose', '3f4'], ['psize_A', 'f4'], ['error', 'f4'], ['error_min', 'f4'], ['resid_pow', 'f4'], ['slice_pow', 'f4'], ['image_pow', 'f4'], ['cross_cor', 'f4'], ['alpha', 'f4'], ['alpha_min', 'f4'], ['weight', 'f4'], ['pose_ess', 'f4'], ['shift_ess', 'f4'], ['class_posterior', 'f4'], ['class', 'u4'], ['class_ess', 'f4']], 'name': 'alignments3D', 'num_items': [], 'passthrough': True, 'title': 'Passthrough alignments3D', 'type': 'particle.alignments3D', 'uid': 'J718-R9', 'versions': []}], 'params_base': {'compute_use_ssd': {'advanced': False, 'desc': 'Use the SSD to cache particles. Speeds up processing significantly.', 'hidden': False, 'order': 16, 'section': 'compute_settings', 'title': 'Cache particle images on SSD', 'type': 'boolean', 'value': True}, 'prepare_window_dataset': {'advanced': False, 'desc': '', 'hidden': False, 'order': 0, 'section': 'prepare', 'title': 'Window dataset (real-space)', 'type': 'boolean', 'value': True}, 'prepare_window_inner_radius': {'advanced': True, 'desc': '', 'hidden': False, 'order': 1, 'section': 'prepare', 'title': 'Window inner radius', 'type': 'number', 'value': 0.85}, 'prepare_window_outer_radius': {'advanced': True, 'desc': '', 'hidden': False, 'order': 2, 'section': 'prepare', 'title': 'Window outer radius', 'type': 'number', 'value': 0.99}, 'random_seed': {'advanced': True, 'desc': 'Randomly set when job is created.', 'hidden': False, 'order': 17, 'section': 'random', 'title': 'Random seed', 'type': 'number', 'value': 1642464893}, 'var_K': {'advanced': False, 'desc': 'The number of orthogonal principle modes (i.e. eigenvectors of the 3D covariance) to solve.', 'hidden': False, 'order': 3, 'section': 'var3D', 'title': 'Number of modes to solve', 'type': 'number', 'value': 3}, 'var_N': {'advanced': False, 'desc': 'The volume size to use for refinement. If this is null, use the full image size. Otherwise images are automatically downsampled', 'hidden': True, 'order': 4, 'section': 'var3D', 'title': 'Refinement box size (Voxels)', 'type': 'number', 'value': None}, 'var_filter_order': {'advanced': False, 'desc': 'Order of filter', 'hidden': False, 'order': 8, 'section': 'var3D', 'title': 'Filter order', 'type': 'number', 'value': 1.5}, 'var_filter_res': {'advanced': False, 'desc': 'Resolution at which results are filtered', 'hidden': False, 'order': 7, 'section': 'var3D', 'title': 'Filter resolution (A)', 'type': 'number', 'value': None}, 'var_highpass_order': {'advanced': True, 'desc': 'Order of filter', 'hidden': False, 'order': 10, 'section': 'var3D', 'title': 'Highpass order', 'type': 'number', 'value': 8}, 'var_highpass_res': {'advanced': True, 'desc': 'Resolution below which variability is ignored', 'hidden': False, 'order': 9, 'section': 'var3D', 'title': 'Highpass resolution (A)', 'type': 'number', 'value': None}, 'var_lambda': {'advanced': True, 'desc': 'Stabilizing coefficient - try larger values if optimization diverges and creates artefacts. In v2.12 this was changed to a normalized fractional value, where 0.01 should work for almost all datasets.', 'hidden': False, 'order': 15, 'section': 'var3D', 'title': 'Lambda', 'type': 'number', 'value': 0.01}, 'var_num_iterations': {'advanced': True, 'desc': 'Number of optimization iterations when solving 3D variability', 'hidden': False, 'order': 14, 'section': 'var3D', 'title': 'Number of iterations', 'type': 'number', 'value': 20}, 'var_num_particles': {'advanced': False, 'desc': '', 'hidden': False, 'order': 6, 'section': 'var3D', 'title': 'Only use this many particles', 'type': 'number', 'value': None}, 'var_symmetry': {'advanced': False, 'desc': 'This symmetry is not actually used in the job. Particles must be symmetry-expanded (use the Symmetry Expansion job) prior to connecting to 3D Variability.', 'hidden': False, 'order': 5, 'section': 'var3D', 'title': 'Symmetry', 'type': 'string', 'value': 'C1'}, 'var_use_gramschmidt': {'advanced': True, 'desc': '', 'hidden': True, 'order': 11, 'section': 'var3D', 'title': 'Use Gram-Schmidt', 'type': 'boolean', 'value': True}, 'var_use_scales': {'advanced': True, 'desc': 'How to treat per-particle scale factors. No scales means all particles have scale 1.0 (useful for very small particles or strange cases). Input scales means to use the input scale factors (which may have come from another refinement). Optimal means to compute per-particle optimal scales on the fly during 3D variability.', 'enum_dict': {'input': 'input', 'none': 'none', 'optimal': 'optimal'}, 'enum_keys': ['none', 'input', 'optimal'], 'hidden': False, 'order': 13, 'section': 'var3D', 'title': 'Per-particle scale', 'type': 'enum', 'value': 'optimal'}, 'var_use_white_noise': {'advanced': True, 'desc': 'Use a white noise model (default) instead of a colored noise model. One or the other may work better depending on the dataset.', 'hidden': False, 'order': 12, 'section': 'var3D', 'title': 'Use white noise model', 'type': 'boolean', 'value': False}}, 'params_secs': {'compute_settings': {'desc': '', 'order': 2, 'title': 'Compute settings'}, 'prepare': {'desc': '', 'order': 0, 'title': 'Particle preprocessing'}, 'random': {'desc': '', 'order': 3, 'title': 'Random Seeds'}, 'var3D': {'desc': '', 'order': 1, 'title': '3D Variability'}}, 'params_spec': {'compute_use_ssd': {'value': False}, 'var_filter_res': {'value': 6}}, 'parents': ['J632'], 'priority': 0, 'project_uid': 'P71', 'project_uid_num': 71, 'queue_index': None, 'queue_message': None, 'queue_status': None, 'queued_at': 'Thu, 14 Dec 2023 16:17:24 GMT', 'queued_job_hash': None, 'queued_to_gpu': False, 'queued_to_hostname': None, 'queued_to_lane': 'htc', 'resources_allocated': {'fixed': {'SSD': False}, 'hostname': 'gpur1.srv-local.mpi-dortmund.mpg.de', 'lane': 'htc', 'lane_type': 'node', 'license': True, 'licenses_acquired': 1, 'slots': {'CPU': [0, 1, 2, 3], 'GPU': [0], 'RAM': [0, 1, 2]}, 'target': {'cache_path': '/mnt/scratch', 'cache_quota_mb': None, 'cache_reserve_mb': 10000, 'desc': None, 'gpus': [{'id': 0, 'mem': 8507949056, 'name': 'NVIDIA GeForce GTX 1080'}, {'id': 1, 'mem': 8507949056, 'name': 'NVIDIA GeForce GTX 1080'}, {'id': 2, 'mem': 8507949056, 'name': 'NVIDIA GeForce GTX 1080'}, {'id': 3, 'mem': 8504934400, 'name': 'NVIDIA GeForce GTX 1080'}], 'hostname': 'gpur1.srv-local.mpi-dortmund.mpg.de', 'lane': 'htc', 'monitor_port': None, 'name': 'gpur1.srv-local.mpi-dortmund.mpg.de', 'resource_fixed': {'SSD': True}, 'resource_slots': {'CPU': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15], 'GPU': [0, 1, 2, 3], 'RAM': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]}, 'ssh_str': 'cryosparc_admin@gpur1.srv-local.mpi-dortmund.mpg.de', 'title': 'Worker node gpur1.srv-local.mpi-dortmund.mpg.de', 'type': 'node', 'worker_bin_path': '/home_local/cryosparc_admin/cryosparc_worker/bin/cryosparcw'}}, 'resources_needed': {'fixed': {'SSD': False}, 'slots': {'CPU': 4, 'GPU': 1, 'RAM': 3}}, 'run_as_user': None, 'running_at': 'Thu, 14 Dec 2023 16:17:33 GMT', 'started_at': 'Thu, 14 Dec 2023 16:17:31 GMT', 'status': 'failed', 'status_num': 40, 'title': 'New Job J718', 'tokens_acquired_at': 1702570645.9293578, 'tokens_requested_at': None, 'type': 'var_3D', 'ui_layouts': {'P71': {'floater': False, 'groups': [], 'height': 192, 'left': 8204, 'show': True, 'top': 8208, 'width': 444}, 'P71W14': {'floater': False, 'groups': [], 'height': 192, 'left': 8204, 'show': True, 'top': 6848, 'width': 444}, 'P71W8': {'floater': False, 'groups': [], 'height': 192, 'left': 0, 'show': False, 'top': 0, 'width': 444}}, 'ui_tile_height': 1, 'ui_tile_images': [], 'ui_tile_width': 3, 'uid': 'J718', 'uid_num': 718, 'version': 'v4.3.1', 'waiting_at': None, 'workspace_uids': ['W14']}
Any input? It would be great to get this running but I have no clue what is going wrong
@MicaelaBS Particle stacks may have been corrupted.
You may try
- a Check For Corrupt Particles job with your particle stacks, with the NaN option enabled
- or continue processing with a re-extracted particle stacks