Description
We tried running spikeinterface on 2 different machines and at the moment of launching kilosort via matlab (we tried different versions of matlab as well) it fails. Matlab briefly opens but it then crashes. Kilosort per se works when used via matlab.
We get the following errors from the jupyter notebook we are using to run the spikeinterface pipeline (we tried a few things but we could not fix it):
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Error running kilosort2_5
SpikeSortingError Traceback (most recent call last)
Cell In[19], line 2
1 # Sorting as a whole
----> 2 sorting = si.run_sorter('kilosort2_5', rec, output_folder=base_folder / 'Paolo-ThinBarTest-Merged/test/kilosort2_5_output',
3 do_correction=True, docker_image=False, verbose=True, raise_error=True,
4 remove_existing_folder=True)
File ~\AppData\Local\Programs\Python\Python310\lib\site-packages\spikeinterface\sorters\runsorter.py:147, in run_sorter(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, docker_image, singularity_image, delete_container_files, with_output, **sorter_params)
140 container_image = singularity_image
141 return run_sorter_container(
142 container_image=container_image,
143 mode=mode,
144 **common_kwargs,
145 )
--> 147 return run_sorter_local(**common_kwargs)
File ~\AppData\Local\Programs\Python\Python310\lib\site-packages\spikeinterface\sorters\runsorter.py:173, in run_sorter_local(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, with_output, **sorter_params)
171 SorterClass.set_params_to_folder(recording, output_folder, sorter_params, verbose)
172 SorterClass.setup_recording(recording, output_folder, verbose=verbose)
--> 173 SorterClass.run_from_folder(output_folder, raise_error, verbose)
174 if with_output:
175 sorting = SorterClass.get_result_from_folder(output_folder)
File ~\AppData\Local\Programs\Python\Python310\lib\site-packages\spikeinterface\sorters\basesorter.py:289, in BaseSorter.run_from_folder(cls, output_folder, raise_error, verbose)
286 print(f"{sorter_name} run time {run_time:0.2f}s")
288 if has_error and raise_error:
--> 289 raise SpikeSortingError(
290 f"Spike sorting error trace:\n{log['error_trace']}\n"
291 f"Spike sorting failed. You can inspect the runtime trace in {output_folder}/spikeinterface_log.json."
292 )
294 return run_time
SpikeSortingError: Spike sorting error trace:
Traceback (most recent call last):
File "C:\Users\sabatini\AppData\Local\Programs\Python\Python310\lib\site-packages\spikeinterface\sorters\basesorter.py", line 254, in run_from_folder
SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
File "C:\Users\sabatini\AppData\Local\Programs\Python\Python310\lib\site-packages\spikeinterface\sorters\external\kilosortbase.py", line 215, 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
Spike sorting failed. You can inspect the runtime trace in D:\Shun\Recordings\Ephys\Paolo-ThinBarTest-Merged\test\kilosort2_5_output/spikeinterface_log.json.
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thank you very much