SpikeInterface / SpikeInterface/spikeinterface
Issue with kilosort2.5 with file size
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Description
Hi, I was running into an issue when sorting an 11gb ns6 file. I previously have tried another 5gb file with no issues. I remember reading another similar issue on github where it was mentioned that it might have to do with the amount of gaps in the recording. There was also a certain software used that could help fix these issues but I also cannot remember the name. My error message is attached below.
SpikeSortingError Traceback (most recent call last)
Cell In[4], [line 16](vscode-notebook-cell:?execution_count=4&line=16)
13 params = {'skip_kilosort_preprocessing': True, 'car': False,'delete_tmp_files': True}
14 params = si.get_default_sorter_params('kilosort2_5')
---> [16](vscode-notebook-cell:?execution_count=4&line=16) sorting = si.run_sorter(sorter_name="kilosort2_5",recording=recording,verbose=True,**params, delete_output_folder=True)
File c:\Users\edtom\anaconda3\Lib\site-packages\spikeinterface\sorters\runsorter.py:198, in run_sorter(sorter_name, recording, folder, remove_existing_folder, delete_output_folder, verbose, raise_error, docker_image, singularity_image, delete_container_files, with_output, output_folder, **sorter_params)
187 raise RuntimeError(
188 "The python `spython` package must be installed to "
189 "run singularity. Install with `pip install spython`"
190 )
192 return run_sorter_container(
193 container_image=container_image,
194 mode=mode,
195 **common_kwargs,
196 )
--> [198](file:///C:/Users/edtom/anaconda3/Lib/site-packages/spikeinterface/sorters/runsorter.py:198) return run_sorter_local(**common_kwargs)
File c:\Users\edtom\anaconda3\Lib\site-packages\spikeinterface\sorters\runsorter.py:260, in run_sorter_local(sorter_name, recording, folder, remove_existing_folder, delete_output_folder, verbose, raise_error, with_output, output_folder, **sorter_params)
258 SorterClass.setup_recording(recording, folder, verbose=verbose)
259 # This NEEDS to happen in the docker because of dependencies
--> [260](file:///C:/Users/edtom/anaconda3/Lib/site-packages/spikeinterface/sorters/runsorter.py:260) SorterClass.run_from_folder(folder, raise_error, verbose)
261 if with_output:
262 sorting = SorterClass.get_result_from_folder(folder, register_recording=True, sorting_info=True)
...
File "c:\Users\edtom\anaconda3\Lib\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
Spike sorting failed. You can inspect the runtime trace in c:\Users\edtom\Downloads\importeddata\kilosort2_5_output/spikeinterface_log.json.`
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by inspecting the attached traceback and the spikeinterface_log.json file at c:\Users\edtom\Downloads\importeddata\kilosort2_5_output, then trace the failure through spikeinterface/sorters/runsorter.py and spikeinterface/sorters/external/kilosortbase.py. Compare the 11 GB and 5 GB recordings and determine whether the failure is reproducible and what concrete change is required.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100