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KudryashevLab / TomoBEAR

TomoBEAR is a configurable and customizable modular pipeline for streamlined processing of cryo-electron tomographic data for subtomogram averaging.
https://github.com/KudryashevLab/TomoBEAR/wiki
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Unrecognized function or variable 'xf_file_destination' in BinStack #24

Closed dacolombo closed 9 months ago

dacolombo commented 9 months ago

Issue type

Bug

TomoBEAR source

source code (via interactive MATLAB session)

TomoBEAR version

v0.4.0

Computing system

HPC cluster (interactive computing node)

Issue description

While running the 80S ribosome (EMPIAR-10064) tutorial (also following the new tutorial youtube videos), I have encountered this error during step 10, BinStacks:

INFO: Creating binned aligned stacks...                                                                                                                                                                                                                                                    
INFO: ctfpahseflip will be run as the requested binning level is lower than stack generated by BatchRunTomo!                                                                                                                                                                               
INFO: Creating tomogram_001_bin_2.ali...                                                                                                                                                                                                                                                   
Error using BinStacks/process                                                                                                                                                                                                                                                              
An UndefinedFunction error was thrown on the workers for 'xf_file_destination'.  This might be because the file containing 'xf_file_destination' is not                                                                                                                                    
accessible on the workers. Use addAttachedFiles(pool, files) to specify the required files to be attached.  For more information, see the documentation                                                                                                                                    
for 'parallel.Pool/addAttachedFiles'.                                                                                                                                                                                                                                                      

Error in iteration (line 52)                                                                                                                                                                                                                                                               
    instantiated_class = instantiated_class.process();

Error in LocalPipeline/execution_parallel (line 559)
            parfor j = 1:length(indices)

Error in LocalPipeline/execute (line 399)
                            [dynamic_configuration_out, tomogram_status{i - 1}] = obj.("execution_" + execution_method)(merged_configuration, obj.pipeline_definition{i}, previous_tomogram_status);

Error in runPipeline (line 149)
            pipeline.execute(starting_tomogram, ending_tomogram, step, gpu);

Error in runTomoBear (line 33)
runPipeline(compute_environment, configuration_path, default_configuration_path, starting_tomogram, ending_tomogram, step, gpu);

Caused by:
    Unrecognized function or variable 'xf_file_destination'.

By running lasterror, the last error in the stack is from here: https://github.com/KudryashevLab/TomoBEAR/blob/14fdf7fb4ed9afa0034a6ed706959d9e0fa2e32a/modules/BinStacks.m#L267

Since I am not an expert in this type of analysis, I am not sure if there is something wrong with the previous steps of my analysis (even though they all run fine and the alignments in step 5 of the tutorial seems fine) or if I need to set different parameters. Also I have noticed that even though this failed, there is a SUCCESS file in each tomogram subdirectory as well as in the 10_BinStacks_1 directory.

I have tried to set the use_aligned_stack to true in the ribosome_empiar_10064_dynamo.json file like this:

"BinStacks": {
    "use_aligned_stack": true
},

So that the variable xf_file_destination wouldn't be used. But this resulted in ctfphasefilp going into segmentation fault:

defocus[51] = 2.598075 microns   defocus2 = 2.501543   angle = -8.08
defocus[52] = 2.646239 microns   defocus2 = 2.559629   angle = 12.20
defocus[53] = 2.470964 microns   defocus2 = 2.313139   angle = -65.30
defocus[54] = 2.705030 microns   defocus2 = 2.405159   angle = 4.64
defocus[55] = 2.791834 microns   defocus2 = 2.548032   angle = -47.98
defocus[56] = 2.627351 microns   defocus2 = 2.579297   angle = -46.18
defocus[57] = 2.604138 microns   defocus2 = 2.412704   angle = -63.52
Slice 1, tilt angle is -60.00 degrees.
stripPixelNum=1920 interPixelNum=2 zeroShift=0.649844 inter-strip shift=0.000159
/home/dacolombo/sw/imod/4.11.23/bin/ctfphaseflip: line 3: 1759009 Segmentation fault      (core dumped) "$IMOD_DIR/bin/realbin/ctfphaseflip" "$@"

Error in BinStacks/process (line 274)
                        executeCommand(command, false, obj.log_file_id);

Error in iteration (line 52)
    instantiated_class = instantiated_class.process();

Error in LocalPipeline/execution_parallel (line 559)
            parfor j = 1:length(indices)

Error in LocalPipeline/execute (line 399)
                            [dynamic_configuration_out, tomogram_status{i - 1}] = obj.("execution_" + execution_method)(merged_configuration, obj.pipeline_definition{i}, previous_tomogram_status);

Error in runPipeline (line 149)
            pipeline.execute(starting_tomogram, ending_tomogram, step, gpu);

Error in runTomoBear (line 33)
runPipeline(compute_environment, configuration_path, default_configuration_path, starting_tomogram, ending_tomogram, step, gpu);

559             parfor j = 1:length(indices)

Do you think I am doing something wrong? Is there something I could do to get this step working?

Thanks for your help!

Input configuration (JSON) file

{
    "general": {
        "gpu": -1,
        "jobs_per_node": 1,
        "gpus_per_node": 2,
        "nodes": [],
        "slurm_execute": true,
        "slurm_node_list": "",
        "slurm_nodes": 0,
        "slurm_nice": 0,
        "slurm_partition": "",
        "slurm_gres": "",
        "slurm_qos": "",
        "slurm_constraint": "",
        "slurm_time": "",
        "slurm_exclusive": true,
        "slurm_flags": "",
        "slurm_gpus": 0,
        "slurm_mem_per_gpu_in_gb": 0,
        "slurm_gpus_per_task": 0,
        "slurm": false,
        "gpu_worker_multiplier": 1,
        "pipeline_location": "/home/dacolombo/tomobear_local_test/TomoBEAR",
        "pipeline_executable": "run_TomoBEAR.sh",
        "sbatch_wrapper": "sbatch.sh",
        "cuda_forward_compatibility": true,
        "random_number_generator_seed": 0,
        "tomogram_output_prefix": "tomogram",
        "tomogram_input_prefix": "",
        "data_path": "",
        "processing_path": "",
        "debug": false,
        "project_name": "TomoBEAR",
        "project_description": "TomoBEAR project description",
        "wipe_cache": false,
        "motion_correction_command": "/home/dacolombo/sw/MotionCor2/bin/MotionCor2", 
        "ctf_correction_command": "/home/dacolombo/sw/gctf/bin/Gctf",
        "ctffind_heredoc_path": "configurations/ctffind_heredoc.sh",
        "double_numbering": true,
        "prefix_position": 0,
        "tomogram_number_position": -1,
        "tilt_number_position": -1,
        "angle_position": -1,
        "date_position": -1,
        "time_position": -1,
        "output_folder": "output",
        "scratch_folder": "scratch",
        "remove_folders": false,
        "tilt_scheme": "dose_symmetric",
        "tilting_step": 3,
        "gold_bead_size_in_nm": 10,
        "rotation_tilt_axis": 85,
        "pretilt_tilt_axis": 0,
        "pid_wait_time": 5,
        "raw_files_folder": "raw_files",
        "fid_files_folder": "fiducial_models",
        "motion_corrected_files_folder": "motion_corrected_mrcs",
        "aligned_tilt_stacks_folder": "aligned_tilt_stacks",
        "ctf_corrected_aligned_tilt_stacks_folder": "ctf_corrected_aligned_tilt_stacks",
        "tilt_stacks_folder": "tilt_stacks",
        "binned_tilt_stacks_folder": "binned_tilt_stacks",
        "binned_aligned_tilt_stacks_folder": "binned_aligned_tilt_stacks",
        "ctf_corrected_binned_aligned_tilt_stacks_folder": "ctf_corrected_binned_aligned_tilt_stacks",
        "tomograms_folder": "tomograms",
        "ctf_corrected_tomograms_folder": "ctf_corrected_tomograms",
        "exact_filtered_tomograms_folder": "exact_filtered_tomograms",
        "binned_tomograms_folder": "binned_tomograms",
        "ctf_corrected_binned_tomograms_folder": "ctf_corrected_binned_tomograms",
        "exact_filtered_ctf_corrected_binned_tomograms_folder": "exact_filtered_ctf_corrected_binned_tomograms",
        "binned_exact_filtered_tomograms_folder": "binned_exact_filtered_tomograms",
        "particles_folder": "particles",
        "particles_table_folder": "particles_table",
        "particles_susan_info_folder": "particles_susan_info",
        "meta_data_folder": "meta_data",
        "dynamo_folder": "dynamo",
        "templates_folder": "templates",
        "gain_correction_folder": "gain_correction",
        "binarized_stacks_folder": "binarized_stacks",
        "ctf_corrected_stack_suffix": "ctfc",
        "ignore_success_files": false,
        "keV": 300,
        "spherical_aberation": 2.7,
        "skip_n_first_projections": 3,
        "nominal_defocus_in_nm": 0,
        "link_files_threshold_in_mb": 1,
        "tilt_type": "single",
        "minimum_files": 15,
        "increase_folder_numbers": false,
        "cpu_fraction": 0.5,
        "tomogram_indices": [],
        "tomogram_begin": 0,
        "tomogram_end": 0,
        "tomogram_step": 1,
        "aligned_stack_binning": 4,
        "pre_aligned_stack_binning": 4,
        "template_matching_binning": 16,
        "reconstruction_thickness": 4000,
        "binnings": [16],
        "ignore_file_system_time_stamps": true,
        "automatic_filename_parts_recognition": true,
        "angle_regex": "_([+-]*\\d+[.]+\\d+)[_.]*",
        "name_regex": "([A-Za-z\\d_]+[A-Za-z]+)",
        "number_regex": "[_]*([\\d]+[_[\\d]*]*)_",
        "name_number_regex": "([A-Za-z\\d_]+[A-Za-z]+)[_]*([\\d]+[_[\\d]*]*)",
        "name_number_regex_backup": "([A-Za-z\\d_]+[A-Za-z]+)[_]*([\\d]+[_[\\d]*]*)_",
        "month_date_time_regex": "_([A-Z][a-z]{2}[\\d]{2})_([\\d]{2}.[\\d]{2}.[\\d]{2})[._]",
        "tomogram_acquisition_time_in_minutes": 70,
        "keep_intermediates": true,
        "reconstruct": "binned",
        "em_clarity_path": "",
        "dynamo_path": "/home/dacolombo/sw/dynamo",
        "astra_path": "",
        "modules": [],
        "duplicated_tilts": "last",
        "ft_bin": 1,
        "expected_symmetrie": "C1",
        "checkpoint_module": false,
        "propagate_failed_stacks": true,
        "first_tilt_angle": "",
        "execute": true,
        "box_size": 1.0,
        "citation": "",
        "susan_particle_batch": 1000,
        "direct_copy": 0,
        "as_boxes": 1,
        "SUSAN_path": "",
        "mask_bandpass": [0, 2, 2],
        "ratio_mask_pixels_based_on_unbinned_pixels": 0.05,
        "use_dose_weighted_particles": false,
        "dose": 0,
        "b_factor_per_projection": 4, 
        "dose_order": [],
        "dt_crop_max_mb": 250000,
        "dt_crop_in_memory": 1,
        "dynamo_allow_padding": true,
        "regenerate_load_modules_file": true,
        "ge_flags": "",
        "qsub_wrapper": "qsub.sh",
        "email": "",
        "ge_queue": "",
        "ge_processing_environment": "smp",
        "ge_time": "",
        "ge_memory_per_processing_element_in_gb": "",
        "ge_gpus": 4,
        "ge_processing_elements": 4,
        "python_envs": "",
        "use_conda": true,
        "mcr_location": "",
        "defocus_limit_factor": 2.5,
        "skip_data_check": false,
        "ld_library_path":"",
        "additional_shell_initialization_script": "",
        "mask_path": "",
        "exclude_projections": 0,
        "dose_weight_first_image": true,
        "even_tilt_stacks_folder": "even_tilt_stacks",
        "odd_tilt_stacks_folder": "odd_tilt_stacks",
        "aligned_even_tilt_stacks_folder": "aligned_even_tilt_stacks",
        "aligned_odd_tilt_stacks_folder": "aligned_odd_tilt_stacks",
        "aligned_dose_weighted_tilt_stacks_folder": "aligned_dose_weighted_tilt_stacks",
        "aligned_dose_weighted_sum_tilt_stacks_folder": "aligned_dose_weighted_sum_tilt_stacks",
        "even_motion_corrected_files_folder": "even_motion_corrected_files",
        "odd_motion_corrected_files_folder": "odd_motion_corrected_files",
        "dose_weighted_motion_corrected_files_folder": "dose_weighted_motion_corrected_files",
        "dose_weighted_sum_motion_corrected_files_folder": "dose_weighted_sum_motion_corrected_files",
        "apply_patch_based_correction_to_all_projections": true,
        "binned_even_tilt_stacks_folder": "binned_even_tilt_stacks",
        "binned_odd_tilt_stacks_folder": "binned_odd_tilt_stacks",
        "binned_aligned_even_tilt_stacks_folder": "binned_aligned_even_tilt_stacks",
        "binned_aligned_odd_tilt_stacks_folder": "binned_aligned_odd_tilt_stacks",
        "binned_aligned_dose_weighted_tilt_stacks_folder": "binned_aligned_dose_weighted_tilt_stacks",
        "binned_aligned_dose_weighted_sum_tilt_stacks_folder": "binned_aligned_dose_weighted_sum_tilt_stacks",
        "even_tomograms_folder": "even_tomograms",
        "odd_tomograms_folder": "odd_tomograms",
        "dose_weighted_tomograms_folder": "dose_weighted_tomograms",
        "dose_weighted_sum_tomograms_folder": "dose_weighted_sum_tomograms",
        "binned_even_tomograms_folder": "binned_even_tomograms",
        "binned_odd_tomograms_folder": "binned_odd_tomograms",
        "ctf_corrected_binned_even_tomograms_folder": "ctf_corrected_binned_even_tomograms",
        "ctf_corrected_binned_odd_tomograms_folder": "ctf_corrected_binned_odd_tomograms",
        "binned_dose_weighted_tomograms_folder": "binned_dose_weighted_tomograms",
        "binned_dose_weighted_sum_tomograms_folder": "binned_dose_weighted_sum_tomograms",
        "ctf_corrected_binned_dose_weighted_tomograms_folder": "ctf_corrected_binned_dose_weighted_tomograms",
        "ctf_corrected_binned_dose_weighted_sum_tomograms_folder": "ctf_corrected_binned_dose_weighted_sum_tomograms",
        "ctf_corrected_binned_aligned_even_tilt_stacks_folder": "ctf_corrected_binned_aligned_even_tilt_stacks",
        "ctf_corrected_binned_aligned_odd_tilt_stacks_folder": "ctf_corrected_binned_aligned_odd_tilt_stacks",
        "ctf_corrected_binned_aligned_dose_weighted_tilt_stacks_folder": "ctf_corrected_binned_aligned_dose_weighted_tilt_stacks",
        "ctf_corrected_binned_aligned_dose_weighted_sum_tilt_stacks_folder": "ctf_corrected_binned_aligned_dose_weighted_sum_tilt_stacks",
        "conda_path": "",
        "matlab_shell": "matlab_shell.sh",
        "denoised_ctf_corrected_tomograms_folder": "denoised_ctf_corrected_tomograms",
        "denoised_ctf_corrected_binned_tomograms_folder": "denoised_ctf_corrected_binned_tomograms",
        "denoised_tomograms_folder": "denoised_tomograms",
        "dose_weighted_tilt_stacks_folder": "dose_weighted_tilt_stacks",
        "dose_weighted_sum_tilt_stacks_folder": "dose_weighted_sum_tilt_stacks",
        "denoised_binned_tomograms_folder": "denoised_binned_tomograms",
        "denoised_tilt_stacks_folder": "denoised_tilt_stacks",
        "aretomo_command": "",
        "listening_time_threshold_in_minutes": 15
    },
    "StopPipeline": {
        "execution_method": "control"
    },
    "TomoAlign": {
        "use_tomowarpalign": true,
        "warp_image_range": "",
        "show_transformed_fiducial_model": true,
        "use_aligned_stack": false,
        "leave_one_out_test": true,
        "sample_thickness": true,
        "use_splines": true,
        "use_3d_motion": true,
        "polynomial_order_in_x": 0,
        "polynomial_order_in_y": 0,
        "polynomial_order_in_z": 0,
        "polynomial_order_for_x_motion": 2,
        "polynomial_order_for_y_motion": 2,
        "polynomial_order_for_z_motion": 2,
        "remove_mixed_polynomial_terms": "z",
        "optimize_alignment": "",
        "reference_image_in_degreese": 0,
        "reconstruct": false
    },
    "Reconstruct": {
        "execution_method": "in_order",
        "reconstruct": "binned",
        "use_ctf_corrected_stack": true,
        "generate_exact_filtered_tomograms": false,
        "exact_filter_size": 1500,
        "generate_nad_filtered_tomograms": false,
        "nad_filter_output_iterations_list": [3],
        "nad_filter_number_of_iterations": -1,
        "nad_filter_sigma_for_smoothing": -1,
        "nad_filter_threshold_for_gradients": -1,
        "use_rawtlt": true,
        "correct_angles": "center",
        "skip": false,
        "citation": "",
        "citation_link": "",
        "doi": ""
    },
    "MetaData":{
        "execution_method": "once",
        "parallel_execution": true,
        "do_statistics": false,
        "skip": false,
        "citation": ""
    },
    "SortFiles": {
        "execution_method": "parallel",
        "starting_tomogram": 1,
        "use_link": true,
        "fixed_number": 0,
        "skip": false,
        "citation": ""
    },
    "MotionCor2": {
        "method": "MotionCor2",
        "execution_method": "in_order",
        "output_postfix": "motioncor2",
        "iterations": 50,
        "tolerance": 0.5,
        "gpu_memory": 0.5,
        "patch": "7 5 15",
        "group": 2,
        "outstack": 0,
        "gain": "",
        "defect": "",
        "dark": "",
        "b_factor": [500, 150],
        "in_fm_motion": 1,
        "apply_dose_weighting": false,
        "fm_dose": 0,
        "split_sum": false,
        "tilt": "",
        "magnification_anisotropy_major_scale": 1,
        "magnification_anisotropy_minor_scale": 1,
        "magnification_anisotropy_major_axis_angle": 360,
        "magnification_anisotropy_major_scale_tmp": 1,
        "magnification_anisotropy_minor_scale_tmp": 1,
        "magnification_anisotropy_major_axis_angle_tmp": 360,
        "split_sum": "false",
        "out_aln": "",
        "initial_dose": "",
        "align": 1,
        "throw": "0",
        "trunc": "0",
        "sum_range": [],
        "fm_ref": -1,
        "skip": false,
        "citation": "",
        "citation_link": "",
        "doi": "",
        "eer_upsampling": 2,
        "fm_int_file": "",
        "eer_total_number_of_fractions": 576,
        "eer_fraction_grouping": 16,
        "eer_exposure_per_fraction": 0.006945
    },
    "CreateStacks": {
        "execution_method": "in_order",
        "slice_suffix": "view",
        "normalization_method": "frames",
        "normalized_postfix": "norm",
        "stack_name": "tiltstack",
        "pixel_intensity_average": 128,
        "pixel_intensity_standard_deviation": 4,
        "border_pixels": 75,
        "skip": false,
        "citation": "",
        "citation_link": "",
        "doi": ""
    },
    "GCTFCtfphaseflipCTFCorrection": {
        "execution_method": "parallel",
        "slice_suffix": "view",
        "slice_folder": "slices",
        "gctf_correction_log_file": "gctf.log",
        "ctf_correction_log_file": "ctf_correction.log",
        "exact_filter_suffix": "ef",
        "tomogram_suffix": "full",
        "rotated_tomogram_suffix": "rotx",
        "generate_exact_filtered_tomograms": true,
        "exact_filter_size": 1500,
        "reconstruction_thickness": 2000,
        "use_aligned_stack": false,
        "do_phase_flip": false,
        "run_ctf_phase_flip": false,
        "reconstruct_tomograms": false,
        "defocus_tolerance": 20,
        "iWidth": 15,
        "maximum_strip_width": 1000,
        "ampContrast": 0.1,
        "defocus_file_version": 3,
        "defocus_file_version_3_flag": 1,
        "use_rawtlt": true,
        "skip": false,
        "citation": "",
        "citation_link": "",
        "doi": "",
        "do_EPA": true,
        "estimated_astigmatism": 1000,
        "ctf_estimation_method": "gctf",
        "fourier_spectrum_size": 1024,
        "resL": 50,
        "resH": 4,
        "defL": 5000,
        "defH": 90000,
        "ctf_preestim_defS": 500,
        "ctf_estim_defS": 100,
        "ctffind_output_suffix": "ctfestim"
    },
    "RefineFiducialModel": {
        "execution_method": "sequential",
        "skip": false,
        "citation": ""
    },
    "BatchRunTomo": {
        "execution_method": "parallel",
        "take_fiducials_from_dynamo": true,
        "generate_seed_model_with_all_fiducials_from_dynamo": true,
        "reconstruct_binned_stacks": false,
        "gold_erasing_extra_diameter": 30,
        "maximum_strip_width": 1000,
        "cpu_machine_list": "",
        "template_file": "configurations/batchruntomo-template.adoc",
        "directive_file_name": "DirectiveFile",
        "starting_step": 0,
        "ending_step": 21,
        "exit_on_error": true,
        "batchruntomo_description": "0: Setup
                 1: Preprocessing
                 2: Cross-correlation alignment
                 3: Prealigned stack
                 4: Patch tracking, autoseeding, or RAPTOR
                 5: Bead tracking
                 6: Alignment 
                 7: Positioning
                 8: Aligned stack generation
                 9: CTF plotting
                 10: 3D gold detection
                 11: CTF correction
                 12: Gold erasing after transforming fiducial model or
                     projecting 3D model
                 13: 2D filtering
                 14: Reconstruction
                 14.5: Postprocessing on a/b axis reconstruction
                 15: Combine setup
                 16: Solvematch
                 17: Initial matchvol;
                 18: Autopatchfit
                 19: Volcombine
                 20: Postprocessing with Trimvol
                 21: NAD (Nonlinear anistropic diffusion)",
        "directives_description": {
            "path": "/path/to/imod/com/directives.csv",
            "link": "https://bio3d.colorado.edu/imod/doc/directives.html"
        },
        "directives": {
            "setupset.copyarg.focus": 0,
            "setupset.copyarg.bfocus": 0,
            "setupset.copyarg.dual": 0,
            "setupset.copyarg.montage": 0,
            "runtime.Preprocessing.any.archiveOriginal": 0,
            "setupset.copyarg.pixel": "<REPLACE>",
            "setupset.copyarg.gold": "<REPLACE>",
            "setupset.copyarg.rotation": "<REPLACE>",
            "setupset.copyarg.userawtlt": 1,
            "setupset.copyarg.extract": 0,
            "setupset.copyarg.voltage": "<REPLACE>",
            "setupset.copyarg.Cs": "<REPLACE>",
            "setupset.copyarg.defocus": "<REPLACE>",
            "runtime.Preprocessing.any.removeXrays": 1,
            "comparam.eraser.ccderaser.LineObjects": 2,
            "comparam.eraser.ccderaser.BoundaryObjects": 3,
            "comparam.eraser.ccderaser.AllSectionObjects": "1-3",
            "comparam.prenewst.newstack.BinByFactor": "<REPLACE>",
            "runtime.RAPTOR.any.useAlignedStack": 1,
            "runtime.RAPTOR.any.numberOfMarkers": 50,
            "runtime.Fiducials.any.trackingMethod": 0,
            "runtime.Fiducials.any.seedingMethod": 1,
            "comparam.track.beadtrack.LightBeads": 0,
            "comparam.track.beadtrack.RoundsOfTracking": 5,
            "runtime.BeadTracking.any.numberOfRuns": 2,
            "comparam.track.beadtrack.SobelFilterCentering": 1,
            "comparam.track.beadtrack.KernelSigmaForSobel": 1.5,
            "comparam.autofidseed.autofidseed.TwoSurfaces": 0,
            "comparam.autofidseed.autofidseed.TargetNumberOfBeads": 20,
            "comparam.autofidseed.autofidseed.AdjustSizes": 1,
            "comparam.align.tiltalign.MagOption": 0,
            "comparam.align.tiltalign.TiltOption": 0,
            "comparam.align.tiltalign.RotOption": "-1",
            "comparam.align.tiltalign.XTiltOption": 0,
            "comparam.align.tiltalign.BeamTiltOption": 0,
            "comparam.newst.newstack.AntialiasFilter": -1,
            "runtime.AlignedStack.any.binByFactor": "<REPLACE>",
            "runtime.AlignedStack.any.correctCTF": 1,
            "runtime.AlignedStack.any.eraseGold": 1,
            "comparam.align.tiltalign.RobustFitting": 1,
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            "predict": {
                "cryolo_command": "cryolo_predict.py",
                "config_json_filepath": "config_cryolo.json",
                "trained_model_filepath": "cryolo_model.h5",
                "threshold": 0.1,
                "test_tomograms_folder": "test_tomograms",
                "test_tomograms_path": "",
                "tomograms_binning": -1,
                "predict_annot_folder": "predict_annot",
                "num_cpu": -1,
                "tracing_search_range": -1,
                "tracing_memory": -1,
                "tracing_min_length": -1
            },
            "export_annotations": {
                "raw_prtcl_coords_dir": "predict_annot/COORDS",
                "per_table_particle_count": -1,
                "total_particle_count": -1
            }
        }
    }
}

Additional info

No response

GPU model and memory

No response

CUDA version(s)

CUDA 11.5.1

Software setup

MATLAB R2022b dynamo v1.1.535 imod v4.11.23 gctf v1.06 motioncor2 v1.6.3

ArtsemiY commented 9 months ago

Dear Daniele (@dacolombo), Thank you for your post. I'm extremely sorry that it took so long to get to your issue! You did everything correct! I found out, that the latest changes introduced a couple of bugs. You may update your code to the patch-release 0.4.1 where the issue was fixed and proceed with the processing. Thank you for your patience! If you need faster help, you may contact me directly by e-mail in the future.

P.S. Please, reopen this issue or open new one if further help is needed.