saving results to phy not working: "Error using - Invalid type of input arguments (should be uint64)"

hi, I'm running kilosort 3 from within SpikeInterface (Python 3.8) on Ubuntu, and it is ALMOST working but then fails at the saving stage with an error I cannot make any sense of. Would really appreciate any input, many thanks in advance.

sorting_KS3 = ss.run_kilosort3(recording_saved,

                          output_folder='results_KS3',

                          verbose=True)

write_binary_recording: 100%|##############################################| 1/1 [00:09<00:00, 9.78s/it]

KilosortBase._run_from_folder <class 'spikeinterface.sorters.kilosort3.kilosort3.Kilosort3Sorter'> RUNNING SHELL SCRIPT: results_KS3/run_kilosort3.sh

                        < M A T L A B (R) >

              Copyright 1984-2021 The MathWorks, Inc.

         R2021a Update 1 (9.10.0.1649659) 64-bit (glnxa64)

                           April 13, 2021

                        < M A T L A B (R) >

              Copyright 1984-2021 The MathWorks, Inc.

         R2021a Update 1 (9.10.0.1649659) 64-bit (glnxa64)

                           April 13, 2021

To get started, type doc.

For product information, visit www.mathworks.com.

welcome!

this works it is a unix machine

Warning: Function isequaln has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isequaln has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function contains has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function contains has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function endsWith has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function endsWith has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function newline has the same name as a MATLAB builtin. We suggest you

rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function newline has the same name as a MATLAB builtin. We suggest you

rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function startsWith has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function startsWith has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isfile has the same name as a MATLAB builtin. We suggest you

rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isfile has the same name as a MATLAB builtin. We suggest you

rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isfolder has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isfolder has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function contains has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function contains has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isfile has the same name as a MATLAB builtin. We suggest you

rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isfile has the same name as a MATLAB builtin. We suggest you

rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isfolder has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isfolder has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isstring has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Warning: Function isstring has the same name as a MATLAB builtin. We suggest

you rename the function to avoid a potential name conflict.

In addpath (line 86)

In startup (line 36)

Time 1s. Computing whitening matrix..

Getting channel whitening matrix...

Channel-whitening matrix computed.

Time 4s. Loading raw data and applying filters...

Time 12s. Finished preprocessing 92 batches.

vertical pitch size is 1.250000e+01

horizontal pitch size is 5

Columns 1 through 3

               0   2.500000000000000   5.000000000000000

Columns 4 through 6

7.500000000000000 10.000000000000000 12.500000000000000

Columns 7 through 9

15.000000000000000 17.500000000000000 20.000000000000000

Column 10

22.500000000000000

Columns 1 through 3

               0   2.500000000000000   5.000000000000000

Columns 4 through 6

7.500000000000000 10.000000000000000 12.500000000000000

Columns 7 through 9

15.000000000000000 17.500000000000000 20.000000000000000

Column 10

22.500000000000000

39

39

0.43 sec, 1 batches, 429 spikes

3.80 sec, 92 batches, 42523 spikes

time 13.76, Shifted up/down 92 batches.

0.13 sec, 1 batches, 484 spikes

4.61 sec, 92 batches, 49326 spikes

time 0.00, GROUP 1/24, units 0

time 18.07, GROUP 6/24, units 29

time 26.40, GROUP 11/24, units 45

time 30.35, GROUP 16/24, units 55

time 34.00, GROUP 21/24, units 65

Elapsed time is 38.482035 seconds.

Time 39s. Final spike extraction ...

39.21 sec, 1 / 92 batches, 77 units, nspks: 517, mu: 15.2878, nst0: 517

Elapsed time is 42.328201 seconds.

time 0.00, GROUP 1/24, units 0

time 14.13, GROUP 6/24, units 27

time 22.42, GROUP 11/24, units 46

time 28.22, GROUP 16/24, units 59

time 31.32, GROUP 21/24, units 66

Elapsed time is 33.115429 seconds.

ans =

initialized spike counts

merged 11 into 9

merged 10 into 9

merged 25 into 30

merged 52 into 48

merged 33 into 31

merged 26 into 30

merged 65 into 48

merged 12 into 9

merged 23 into 29

merged 44 into 48

merged 51 into 53

merged 27 into 30

merged 66 into 48

merged 64 into 48

merged 70 into 59

ans =

Saving results to Phy

--------------------------------------------------------------------------------Error using -

Invalid type of input arguments (should be uint64)Error using -

Invalid type of input arguments (should be uint64) Error running kilosort3 Traceback (most recent call last): File "/home/john/miniconda3/envs/si/lib/python3.8/site-packages/spikeinterface-0.92.1.dev0-py3.8.egg/spikeinterface/sorters/basesorter.py", line 200, in run_from_folder SorterClass._run_from_folder(output_folder, sorter_params, verbose) File "/home/john/miniconda3/envs/si/lib/python3.8/site-packages/spikeinterface-0.92.1.dev0-py3.8.egg/spikeinterface/sorters/kilosortbase.py", line 42, in _run_from_folder raise Exception(f'{cls.sorter_name} returned a non-zero exit code') Exception: kilosort3 returned a non-zero exit code

SpikeSortingError Traceback (most recent call last) /tmp/ipykernel_337534/2606529102.py in ----> 1 sorting_KS3 = ss.run_kilosort3(recording_saved, 2 output_folder='results_KS3', 3 verbose=True)

~/miniconda3/envs/si/lib/python3.8/site-packages/spikeinterface-0.92.1.dev0-py3.8.egg/spikeinterface/sorters/runsorter.py in run_kilosort3(*args, kwargs) 368 369 def run_kilosort3(*args, *kwargs): --> 370 return run_sorter('kilosort3', args, kwargs) 371 372

~/miniconda3/envs/si/lib/python3.8/site-packages/spikeinterface-0.92.1.dev0-py3.8.egg/spikeinterface/sorters/runsorter.py in run_sorter(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, docker_image, with_output, **sorter_params) 55 56 if docker_image is None: ---> 57 sorting = run_sorter_local(sorter_name, recording, output_folder=output_folder, 58 remove_existing_folder=remove_existing_folder, 59 delete_output_folder=delete_output_folder,

~/miniconda3/envs/si/lib/python3.8/site-packages/spikeinterface-0.92.1.dev0-py3.8.egg/spikeinterface/sorters/runsorter.py in run_sorter_local(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, with_output, **sorter_params) 84 recording, output_folder, sorter_params, verbose) 85 SorterClass.setup_recording(recording, output_folder, verbose=verbose) ---> 86 SorterClass.run_from_folder(output_folder, raise_error, verbose) 87 if with_output: 88 sorting = SorterClass.get_result_from_folder(output_folder)

~/miniconda3/envs/si/lib/python3.8/site-packages/spikeinterface-0.92.1.dev0-py3.8.egg/spikeinterface/sorters/basesorter.py in run_from_folder(cls, output_folder, raise_error, verbose) 234 if has_error and raise_error: 235 print(log['error_trace']) --> 236 raise SpikeSortingError( 237 f"Spike sorting failed. You can inspect the runtime trace in {output_folder}/spikeinterface_log.json") 238

SpikeSortingError: Spike sorting failed. You can inspect the runtime trace in results_KS3/spikeinterface_log.json

cortex-lab / KiloSort

saving results to phy not working: "Error using - Invalid type of input arguments (should be uint64)" #249