paramset 1 - spykingcircus2 - `SpikeSortingError: Spike sorting error `

[MilagrosMarin]

{'table_name': '_s_i_clustering',
 'key_hash': '9e35f7209400f9868fe51995cc2e8097',
 'status': 'error',
 'key': {'organoid_id': 'O09',
  'experiment_start_time': datetime.datetime(2023, 5, 3, 17, 33),
  'insertion_number': 0,
  'start_time': datetime.datetime(2023, 5, 11, 4, 22),
  'end_time': datetime.datetime(2023, 5, 11, 4, 27),
  'paramset_idx': 1},
 'error_message': 'SpikeSortingError: Spike sorting error trace:\nTraceback (most recent call last):\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sorters/basesorter.py", line 270, in run_from_folder\n    SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sorters/internal/spyking_circus2.py", line 323, in _run_from_folder\n    outputs = find_cluster_from_peaks(\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sortingcomponents/clustering/main.py", line 44, in find_cluster_from_peaks\n    outputs = method_class.main_function(recording, peaks, params, job_kwargs=job_kwargs)\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sortingcomponents/clustering/graph_clustering.py", line 91, in main_function\n    distances = create_graph_from_peak_features(\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sortingcomponents/clustering/graph_tools.py", line 219, in create_graph_from_peak_features\n    ind0, ind1 = distances.tocoo().coords\nAttributeError: \'coo_matrix\' object has no attribute \'coords\'\n\nSpike sorting failed. You can inspect the runtime trace in [/mnt/efs/works/org/utah/proj/organoids/outbox/O09-12_raw/202305110422_202305110427/O09/spykingcircus2_1/spykingcircus2/spike_sorting/spikeinterface_log.json.](https://file+.vscode-resource.vscode-cdn.net/mnt/efs/works/org/utah/proj/organoids/outbox/O09-12_raw/202305110422_202305110427/O09/spykingcircus2_1/spykingcircus2/spike_sorting/spikeinterface_log.json.)',
 'error_stack': 'Traceback (most recent call last):\n  File "/opt/conda/lib/python3.10/site-packages/datajoint/autopopulate.py", line 397, in _populate1\n    make(dict(key), **(make_kwargs or {}))\n  File "/opt/conda/lib/python3.10/site-packages/element_array_ephys/spike_sorting/si_spike_sorting.py", line 278, in make\n    _run_sorter()\n  File "/opt/conda/lib/python3.10/site-packages/element_interface/utils.py", line 235, in wrapped\n    results = func(*args, **kwargs)\n  File "/opt/conda/lib/python3.10/site-packages/element_array_ephys/spike_sorting/si_spike_sorting.py", line 264, in _run_sorter\n    si_sorting: si.sorters.BaseSorter = si.sorters.run_sorter(\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sorters/runsorter.py", line 202, in run_sorter\n    return run_sorter_local(**common_kwargs)\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sorters/runsorter.py", line 294, in run_sorter_local\n    SorterClass.run_from_folder(folder, raise_error, verbose)\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sorters/basesorter.py", line 310, in run_from_folder\n    raise SpikeSortingError(\nspikeinterface.sorters.utils.misc.SpikeSortingError: Spike sorting error trace:\nTraceback (most recent call last):\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sorters/basesorter.py", line 270, in run_from_folder\n    SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sorters/internal/spyking_circus2.py", line 323, in _run_from_folder\n    outputs = find_cluster_from_peaks(\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sortingcomponents/clustering/main.py", line 44, in find_cluster_from_peaks\n    outputs = method_class.main_function(recording, peaks, params, job_kwargs=job_kwargs)\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sortingcomponents/clustering/graph_clustering.py", line 91, in main_function\n    distances = create_graph_from_peak_features(\n  File "/opt/conda/lib/python3.10/site-packages/spikeinterface/sortingcomponents/clustering/graph_tools.py", line 219, in create_graph_from_peak_features\n    ind0, ind1 = distances.tocoo().coords\nAttributeError: \'coo_matrix\' object has no attribute \'coords\'\n\nSpike sorting failed. You can inspect the runtime trace in /mnt/efs/works/org/utah/proj/organoids/outbox/O09-12_raw/202305110422_202305110427/O09/spykingcircus2_1/spykingcircus2/spike_sorting/spikeinterface_log.json.\n',
 'timestamp': datetime.datetime(2025, 7, 29, 11, 50, 57)}

{'paramset_idx': 1,
 'clustering_method': 'spykingcircus2',
 'paramset_desc': 'Default parameter set for spyking circus2 using SpikeInterface v0.101.*',
 'param_set_hash': UUID('434894d0-eb7b-db6c-80e6-638a1322c568'),
 'params': {'SI_PREPROCESSING_METHOD': 'organoid_preprocessing',
  'SI_SORTING_PARAMS': {'general': {'ms_before': 2,
    'ms_after': 2,
    'radius_um': 100},
   'filtering': {'freq_min': 150},
   'detection': {'peak_sign': 'neg', 'detect_threshold': 4},
   'selection': {'method': 'smart_sampling_amplitudes',
    'n_peaks_per_channel': 5000,
    'min_n_peaks': 20000,
    'select_per_channel': False},
   'clustering': {'legacy': False},
   'matching': {'method': 'circus-omp-svd', 'method_kwargs': {}},
   'apply_preprocessing': True,
   'cache_preprocessing': {'mode': 'memory',
    'memory_limit': 0.5,
    'delete_cache': True},
   'multi_units_only': False,
   'job_kwargs': {'n_jobs': 0.8},
   'debug': False},
  'SI_POSTPROCESSING_PARAMS': {'extensions': {'random_spikes': {},
    'waveforms': {},
    'templates': {},
    'noise_levels': {},
    'correlograms': {},
    'isi_histograms': {},
    'principal_components': {'n_components': 5, 'mode': 'by_channel_local'},
    'spike_amplitudes': {},
    'spike_locations': {},
    'template_metrics': {'include_multi_channel_metrics': True},
    'template_similarity': {},
    'unit_locations': {},
    'quality_metrics': {}},
   'job_kwargs': {'n_jobs': -1, 'chunk_duration': '1s'},
   'export_to_phy': True,
   'export_report': True}}}