Hi all,
I tried to follow the Ewald sphere correction tutorial given in the website. The procedure seems to be straight forward. But I don’t get reconstruction at the end. There seem to be no errors, which could help me debug the issue. Are there any pre-processing steps that need to be done, not mentioned in the tutorial?
I only get these warnings
The FSC plot is a horizontal line below 0.2. (Sorry, I am not allowed to upload a second image. )
Welcome to the forum @vi1.
Please can you post (as text, to facilitate forum searches) the outputs of these commands
cryosparcm cli "get_job('P99', 'J199', 'job_type', 'version', 'params_spec', 'instance_information', 'input_slot_groups')"
cryosparcm eventlog P99 J199 | tail -n 40
for
with project ID P99, job ID J199 replaced correspondingly.
Here are the outputs:
1. Import Particles Job:
{'_id': '669c1897eaf89f77923fb742', 'input_slot_groups': [{'connections': [], 'count_max': inf, 'count_min': 0, 'description': 'Optional, micrographs from which these partiles were extracted. Providing this input causes the import job to make correspondences between the filename of the inputted micrographs, and the rlnMicrographName in the imported star file of particles. Filenames are matched up the a specified number of chars.', 'name': 'micrographs', 'repeat_allowed': False, 'slots': [{'description': '', 'name': 'micrograph_blob', 'optional': False, 'title': 'Source Exposure data', 'type': 'exposure.micrograph_blob'}], 'title': 'Source Exposures', 'type': 'exposure'}], 'instance_information': {'available_memory': '119.09GB', 'cpu_model': 'Intel(R) Core(TM) i9-10940X CPU @ 3.30GHz', 'ofd_hard_limit': 1048576, 'ofd_soft_limit': 1024, 'physical_cores': 14, 'platform_architecture': 'x86_64', 'platform_node': 'dmi-20-pc-32', 'platform_release': '5.15.0-116-generic', 'platform_version': '#126~20.04.1-Ubuntu SMP Mon Jul 1 15:40:07 UTC 2024', 'total_memory': '125.48GB', 'used_memory': '4.77GB'}, 'job_type': 'import_particles', 'params_spec': {'alignments3D_exists': {'value': True}, 'blob_exists': {'value': True}, 'ctf_exists': {'value': True}, 'enable_validation': {'value': True}, 'particle_blob_path': {'value': '/CryoEM/data/2017-12-27_MagCorrect_Frames05-19.mrcs'}, 'particle_meta_path': {'value': '/CryoEM/data/2017-12-27_MagCorrect_Frames05-19_Numbered_adjusted.star'}}, 'project_uid': 'P1', 'uid': 'J9', 'version': 'v4.5.3'}
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 319 MB] Reading rlnImageName to get indices and paths..
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] Warning: Parameter particle_blob_path was set, which overrides rlnImageName despite the latter being present in the input star file.
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] Parameter particle_blob_path was set and is a file, so will override the rlnImageName
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] Parameter particle_blob_path was set and is a file, but rlnImageName also exists. In this case, the indices of particles within .mrc files will be kept from rlnImageName, but the .mrc path will be overrriden by particle_blob_path
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] Searching for linked data files...
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] Compiling CTF information...
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 333 MB] Warning: No exposures were connected as inputs, so correspondences cannot be found, so output will not contain pick locations for particles.
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 333 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 333 MB] Compiling particle pose information...
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 333 MB] Converting euler angles..
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] Particle information has now been imported for 30515 particles, creating outputs...
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] Found references to 1 unique data files
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] Import paths were unique at level -1
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] Example imported relative path:
J9/imported/007256896994728514508_2017-12-27_MagCorrect_Frames05-19.mrcs
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] Reading MRC file header to check shape...
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] Validating outputs...
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] All expected outputs were produced.
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] Loaded 30515 particles.
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] Common fields:
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] ctf/accel_kv : {300.0}
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] ctf/cs_mm : {2.7}
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] ctf/amp_contrast : {0.07}
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] ctf/exp_group_id : {3}
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] blob/psize_A : {0.788}
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] blob/shape : [800 800]
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:59 GMT] [CPU RAM used: 355 MB] Making plots...
[Mon, 22 Jul 2024 06:24:03 GMT] Lowpass Filtered Images:
[Mon, 22 Jul 2024 06:24:06 GMT] Raw Images:
[Mon, 22 Jul 2024 06:24:08 GMT] [CPU RAM used: 729 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:24:08 GMT] [CPU RAM used: 729 MB] Compiling job outputs...
[Mon, 22 Jul 2024 06:24:08 GMT] [CPU RAM used: 718 MB] Updating job size...
[Mon, 22 Jul 2024 06:24:08 GMT] [CPU RAM used: 718 MB] Exporting job and creating csg files...
[Mon, 22 Jul 2024 06:24:08 GMT] [CPU RAM used: 718 MB] ***************************************************************
[Mon, 22 Jul 2024 06:24:08 GMT] [CPU RAM used: 718 MB] Job complete. Total time 12.68s
2. Homogeneous Reconstruction Only
{'_id': '669c203bcd123793903689a7', 'input_slot_groups': [{'connections': [{'group_name': 'imported_particles', 'job_uid': 'J9', 'slots': [{'group_name': 'imported_particles', 'job_uid': 'J9', 'result_name': 'blob', 'result_type': 'particle.blob', 'slot_name': 'blob', 'version': 'F'}, {'group_name': 'imported_particles', 'job_uid': 'J9', 'result_name': 'ctf', 'result_type': 'particle.ctf', 'slot_name': 'ctf', 'version': 'F'}, {'group_name': 'imported_particles', 'job_uid': 'J9', '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 3D alignments', 'type': 'particle.alignments3D'}], 'title': 'Particle stacks', 'type': 'particle'}, {'connections': [], 'count_max': 1, 'count_min': 0, 'description': '', 'name': 'mask', 'repeat_allowed': False, 'slots': [{'description': '', 'name': 'mask', 'optional': False, 'title': 'Mask', 'type': 'volume.blob'}], 'title': 'Static mask', 'type': 'mask'}], 'instance_information': {'CUDA_version': '11.8', 'available_memory': '119.07GB', 'cpu_model': 'Intel(R) Core(TM) i9-10940X CPU @ 3.30GHz', 'driver_version': '12.2', 'gpu_info': [{'id': 0, 'mem': 25438126080, 'name': 'NVIDIA GeForce RTX 3090', 'pcie': '0000:17:00'}, {'id': 1, 'mem': 25435242496, 'name': 'NVIDIA GeForce RTX 3090', 'pcie': '0000:65:00'}], 'ofd_hard_limit': 1048576, 'ofd_soft_limit': 1024, 'physical_cores': 14, 'platform_architecture': 'x86_64', 'platform_node': 'dmi-20-pc-32', 'platform_release': '5.15.0-116-generic', 'platform_version': '#126~20.04.1-Ubuntu SMP Mon Jul 1 15:40:07 UTC 2024', 'total_memory': '125.48GB', 'used_memory': '4.79GB'}, 'job_type': 'homo_reconstruct', 'params_spec': {'compute_use_ssd': {'value': False}, 'refine_ignore_tetra': {'value': True}, 'refine_ignore_trefoil': {'value': True}}, 'project_uid': 'P1', 'uid': 'J13', 'version': 'v4.5.3'}
[Mon, 22 Jul 2024 06:25:45 GMT] [CPU RAM used: 6451 MB] Processed 30515.000 images in 78.927s.
[Mon, 22 Jul 2024 06:26:07 GMT] [CPU RAM used: 14524 MB] Computing FSCs...
[Mon, 22 Jul 2024 06:26:07 GMT] [CPU RAM used: 14524 MB] Using full box size 800, downsampled box size 400, with low memory mode disabled.
[Mon, 22 Jul 2024 06:26:07 GMT] [CPU RAM used: 14524 MB] Computing FFTs on GPU.
[Mon, 22 Jul 2024 06:26:20 GMT] [CPU RAM used: 18477 MB] Done in 13.623s
[Mon, 22 Jul 2024 06:26:20 GMT] [CPU RAM used: 18477 MB] Computing cFSCs...
[Mon, 22 Jul 2024 06:26:32 GMT] [CPU RAM used: 18477 MB] Done in 11.572s
[Mon, 22 Jul 2024 06:26:33 GMT] [CPU RAM used: 21414 MB] Filtering at 1.586A
[Mon, 22 Jul 2024 06:27:13 GMT] [CPU RAM used: 33871 MB] Guinier estimation...
[Mon, 22 Jul 2024 06:28:09 GMT] [CPU RAM used: 41764 MB] Plotting..
[Mon, 22 Jul 2024 06:28:59 GMT] Real Space Slices Iteration
[Mon, 22 Jul 2024 06:29:03 GMT] Fourier Space Slices Iteration
[Mon, 22 Jul 2024 06:29:04 GMT] Real Space Mask Slices Iteration
[Mon, 22 Jul 2024 06:29:05 GMT] FSC Iteration
[Mon, 22 Jul 2024 06:29:06 GMT] cFSCs (Half-angle: 20°), with generated tight mask
[Mon, 22 Jul 2024 06:29:35 GMT] Guinier Plot Iteration
[Mon, 22 Jul 2024 06:29:36 GMT] Viewing Direction Distribution
[Mon, 22 Jul 2024 06:29:37 GMT] Posterior Precision Directional Distribution
[Mon, 22 Jul 2024 06:29:37 GMT] Per particle scale factors
[Mon, 22 Jul 2024 06:29:37 GMT] [CPU RAM used: 48146 MB] Done in 88.209s.
[Mon, 22 Jul 2024 06:29:37 GMT] [CPU RAM used: 48146 MB] Outputting files..
[Mon, 22 Jul 2024 06:30:23 GMT] [CPU RAM used: 56468 MB] Done in 46.123s.
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 56468 MB] ====== Done Reconstruction ======
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 56468 MB] Full run took 359.097s
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 11998 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 11998 MB] Compiling job outputs...
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 11998 MB] Passing through outputs for output group particles from input group particles
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 11999 MB] This job outputted results ['alignments3D']
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 11999 MB] Loaded output dset with 30515 items
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 11999 MB] Passthrough results ['blob', 'ctf']
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 11999 MB] Loaded passthrough dset with 30515 items
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 12003 MB] Intersection of output and passthrough has 30515 items
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 12003 MB] Output dataset contains: ['ctf', 'blob']
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 12003 MB] Outputting passthrough result blob
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 12003 MB] Outputting passthrough result ctf
[Mon, 22 Jul 2024 06:30:24 GMT] [CPU RAM used: 12003 MB] Checking outputs for output group particles
[Mon, 22 Jul 2024 06:30:25 GMT] [CPU RAM used: 12006 MB] Updating job size...
[Mon, 22 Jul 2024 06:30:25 GMT] [CPU RAM used: 12006 MB] Exporting job and creating csg files...
[Mon, 22 Jul 2024 06:30:25 GMT] [CPU RAM used: 12006 MB] ***************************************************************
[Mon, 22 Jul 2024 06:30:25 GMT] [CPU RAM used: 12006 MB] Job complete. Total time 359.58s
Thanks @vi1 for posting this information. Please can you additionally post the top portions of the event logs for the J9 and J13 jobs:
cryosparcm eventlog P1 J9 | head -n 50
cryosparcm eventlog P1 J13 | head -n 50
as well as screenshots of the volume slices
Here are the outputs:
1. cryosparcm eventlog P1 J9 | head -n 50
[Mon, 22 Jul 2024 06:23:50 GMT] License is valid.
[Mon, 22 Jul 2024 06:23:50 GMT] Launching job on lane default target localhost ...
[Mon, 22 Jul 2024 06:23:50 GMT] Running job on master node hostname localhost
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] Job J9 Started
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] Master running v4.5.3, worker running v4.5.3
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] Working in directory: /CryoEM/ewald/CS-ewald-sphere/J9
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] Running on lane default
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] Resources allocated:
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] Worker: localhost
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] CPU : [0]
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] GPU : [ ]
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] RAM : [0, 1, 2]
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] SSD : False
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:51 GMT] [CPU RAM used: 92 MB] Importing job module for job type import_particles...
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 309 MB] Job ready to run
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 309 MB] ***************************************************************
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 309 MB] Importing particles from /CryoEM/data/2017-12-27_MagCorrect_Frames05-19_Numbered_adjusted.star
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 310 MB] File extension is star
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 310 MB] Importing star file.
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 319 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 319 MB] Loaded star file with 30515 items
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 319 MB] Fields loaded from star file: ['rlnRandomSubset', 'rlnVoltage', 'rlnDefocusAngle', 'rlnSphericalAberration', 'rlnDetectorPixelSize', 'rlnDefocusU', 'rlnDefocusV', 'rlnMagnification', 'rlnPhaseShift', 'rlnAmplitudeContrast', 'rlnImageName', 'rlnAngleRot', 'rlnAngleTilt', 'rlnAnglePsi', 'rlnOriginX', 'rlnOriginY', 'rlnClassNumber', 'rlnMicrographName', 'rlnCoordinateX', 'rlnCoordinateY', 'rlnGroupNumber', 'rlnGroupName']
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 319 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 319 MB] Reading particle data locations...
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 319 MB] Reading rlnImageName to get indices and paths..
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] Warning: Parameter particle_blob_path was set, which overrides rlnImageName despite the latter being present in the input star file.
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] Parameter particle_blob_path was set and is a file, so will override the rlnImageName
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] Parameter particle_blob_path was set and is a file, but rlnImageName also exists. In this case, the indices of particles within .mrc files will be kept from rlnImageName, but the .mrc path will be overrriden by particle_blob_path
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] Searching for linked data files...
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 331 MB] Compiling CTF information...
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 333 MB] Warning: No exposures were connected as inputs, so correspondences cannot be found, so output will not contain pick locations for particles.
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 333 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 333 MB] Compiling particle pose information...
[Mon, 22 Jul 2024 06:23:56 GMT] [CPU RAM used: 333 MB] Converting euler angles..
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] Particle information has now been imported for 30515 particles, creating outputs...
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] Found references to 1 unique data files
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] Import paths were unique at level -1
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] Example imported relative path:
J9/imported/007256896994728514508_2017-12-27_MagCorrect_Frames05-19.mrcs
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 342 MB] Reading MRC file header to check shape...
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] Validating outputs...
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] All expected outputs were produced.
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] Loaded 30515 particles.
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] Common fields:
[Mon, 22 Jul 2024 06:23:58 GMT] [CPU RAM used: 355 MB] ctf/accel_kv : {300.0}
2. cryosparcm eventlog P1 J13 | head -n 50
[Mon, 22 Jul 2024 06:24:19 GMT] License is valid.
[Mon, 22 Jul 2024 06:24:19 GMT] Launching job on lane default target localhost ...
[Mon, 22 Jul 2024 06:24:19 GMT] Running job on master node hostname localhost
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] Job J13 Started
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] Master running v4.5.3, worker running v4.5.3
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] Working in directory: /CryoEM/ewald/CS-ewald-sphere/J13
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] Running on lane default
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] Resources allocated:
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] Worker: localhost
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] CPU : [0, 1, 2, 3]
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] GPU : [0]
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] RAM : [0, 1, 2]
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] SSD : False
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] --------------------------------------------------------------
[Mon, 22 Jul 2024 06:24:20 GMT] [CPU RAM used: 92 MB] Importing job module for job type homo_reconstruct...
[Mon, 22 Jul 2024 06:24:25 GMT] [CPU RAM used: 327 MB] Job ready to run
[Mon, 22 Jul 2024 06:24:25 GMT] [CPU RAM used: 327 MB] ***************************************************************
[Mon, 22 Jul 2024 06:24:25 GMT] [CPU RAM used: 356 MB] IGNORING trefoil
[Mon, 22 Jul 2024 06:24:25 GMT] [CPU RAM used: 356 MB] IGNORING tetra
[Mon, 22 Jul 2024 06:24:25 GMT] [CPU RAM used: 356 MB] Using random seed of 691211190
[Mon, 22 Jul 2024 06:24:25 GMT] [CPU RAM used: 356 MB] Loading a ParticleStack with 30515 items...
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 369 MB] Done.
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 369 MB] Windowing particles
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Done.
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] ====== Gold Standard Split ======
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Particles have input alignments3D connected, so reusing pre-existing split
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Set A is greater than set B by 1 particles (0.00328 percent difference relative to the total dataset).
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Split A has 15258 particles
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Split B has 15257 particles
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] ====== Reconstruction ======
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Input particles have box size 800
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Input particles have pixel size 0.7880
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Volume refinement will be done with effective box size 800
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Volume refinement will be done with pixel size 0.7880
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Particles will be zeropadded/truncated to size 800 during backprojection
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] Particles will be backprojected with box size 800
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] C1 symmetry group specified.
[Mon, 22 Jul 2024 06:24:26 GMT] [CPU RAM used: 370 MB] -- THR 0 BATCH 500 NUM 15257 TOTAL 30.453377 ELAPSED 75.720775 --
[Mon, 22 Jul 2024 06:25:45 GMT] [CPU RAM used: 6451 MB] Processed 30515.000 images in 78.927s.
[Mon, 22 Jul 2024 06:26:07 GMT] [CPU RAM used: 14524 MB] Computing FSCs...
[Mon, 22 Jul 2024 06:26:07 GMT] [CPU RAM used: 14524 MB] Using full box size 800, downsampled box size 400, with low memory mode disabled.
[Mon, 22 Jul 2024 06:26:07 GMT] [CPU RAM used: 14524 MB] Computing FFTs on GPU.
[Mon, 22 Jul 2024 06:26:20 GMT] [CPU RAM used: 18477 MB] Done in 13.623s
[Mon, 22 Jul 2024 06:26:20 GMT] [CPU RAM used: 18477 MB] Computing cFSCs...
[Mon, 22 Jul 2024 06:26:32 GMT] [CPU RAM used: 18477 MB] Done in 11.572s
[Mon, 22 Jul 2024 06:26:33 GMT] [CPU RAM used: 21414 MB] Filtering at 1.586A
[Mon, 22 Jul 2024 06:27:13 GMT] [CPU RAM used: 33871 MB] Guinier estimation...
[Mon, 22 Jul 2024 06:28:09 GMT] [CPU RAM used: 41764 MB] Plotting..
[Mon, 22 Jul 2024 06:28:59 GMT] Real Space Slices Iteration
[Mon, 22 Jul 2024 06:29:03 GMT] Fourier Space Slices Iteration
3. The screenshots
Hey, thank you for looking into it. Some of the particles had NaN values, which caused the issue. The job didn’t indicate this anywhere. However, when I tried ab-initio reconstruction, the ab-initio job threw an error. I downloaded the file again, and now it seems to work.
Also, how do I know what algorithm is being used in the homogenous reconstruction only job?
Thanks.
