Kilosort 2.5 Index in position 1 exceeds array bounds. Index must not exceed 32.

I have a similar problem to #3204. Unlike the issue, I am currently using 32 channels.

recording = se.BinaryRecordingExtractor(file_paths=[path], sampling_frequency=30000, num_channels=32, dtype='int16')
probe = generate_linear_probe(num_elec=32, ypitch=100.0, contact_shapes="circle", contact_shape_params={"radius":5})
probe.set_device_channel_indices(np.arange(recording.get_num_channels()))
assert recording.get_num_channels() == 32
assert recording.get_channel_locations().shape == (32, 2)
recording = recording.set_probe(probe, in_place=False)

sorting_KS2_5 = ss.run_sorter(sorter_name="kilosort2_5", recording=recording, remove_existing_folder=True, 
    folder=dirname, verbose=True, do_correction=False, preclust_threshold=6, freq_min=200.)

I double checked that the number of channels (i.e., recording.get_num_channels()) is 32. However, I am facing an error that "----------------------------------------Index in position 1 exceeds array bounds. Index must not exceed 32.\u001b[?1l\u001b>"

spikeinterface_log.json shows:

{
    "sorter_name": "kilosort2_5",
    "sorter_version": "git-f2e570c61b6e",
    "datetime": "2025-08-25T20:20:52.738731",
    "runtime_trace": [
        "\u001b[?1h\u001b=",
        "< M A T L A B (R) >",
        "Copyright 1984-2024 The MathWorks, Inc.",
        "R2024a (24.1.0.2537033) 64-bit (glnxa64)",
        "February 21, 2024",
        "",
        "",
        "To get started, type doc.",
        "For product information, visit www.mathworks.com.",
        "",
        "\u001b[?1h\u001b=Time   0s. Computing whitening matrix..",
        "Getting channel whitening matrix...",
        "Channel-whitening matrix computed.",
        "Time   8s. Loading raw data and applying filters...",
        "Time 199s. Finished preprocessing 8493 batches.",
        "Drift correction DISABLED",
        "pitch is 100 um",
        "----------------------------------------Index in position 1 exceeds array bounds. Index must not exceed 32.\u001b[?1l\u001b>"
    ],
    "error": true,
    "error_trace": [
        "Traceback (most recent call last):",
        "  File \"/om2/user/jdhwang/anaconda3/envs/kilosort/lib/python3.9/site-packages/spikeinterface/sorters/basesorter.py\", line 270, in run_from_folder",
        "    SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)",
        "  File \"/om2/user/jdhwang/anaconda3/envs/kilosort/lib/python3.9/site-packages/spikeinterface/sorters/external/kilosortbase.py\", line 217, in _run_from_folder",
        "    raise Exception(f\"{cls.sorter_name} returned a non-zero exit code\")",
        "  Exception: kilosort2_5 returned a non-zero exit code"
    ],
    "run_time": null
}

For your information, I am using spikeinterface version 0.103.0

Reproduce the failure with the shown ss.run_sorter("kilosort2_5", ...) configuration and inspect sorter_output_folder/spikeinterface_log.json. Trace the handoff through spikeinterface/sorters/basesorter.py and spikeinterface/sorters/external/kilosortbase.py, then verify that a 32-channel recording completes without the MATLAB array-bounds error.