spikesorting issue

[mariapfj]

getting an error when spikesorting \projects\ec109\maria\novel-env-nwb\actions\148-300921-2

Postprocessing
Extracting waveforms
Computing QC metrics
Exporting to phy
ERROR: unable to process 148-300921-2
Traceback (most recent call last):
File "/fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/widgets/process.py", line 296, in on_run
process.process_ecephys(
File "/fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/scripts/process.py", line 274, in process_ecephys
shutil.rmtree(phy_folder)
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/shutil.py", line 752, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/shutil.py", line 672, in _rmtree_safe_fd
_rmtree_safe_fd(dirfd, fullname, onerror)
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/shutil.py", line 672, in _rmtree_safe_fd
_rmtree_safe_fd(dirfd, fullname, onerror)
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/shutil.py", line 672, in _rmtree_safe_fd
_rmtree_safe_fd(dirfd, fullname, onerror)
[Previous line repeated 2 more times]
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/shutil.py", line 683, in _rmtree_safe_fd
onerror(os.rmdir, fullname, sys.exc_info())
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/shutil.py", line 681, in _rmtree_safe_fd
os.rmdir(entry.name, dir_fd=topfd)
OSError: [Errno 39] Directory not empty: '_get_correlograms'

[mariapfj]

just tried to process it again and for some reason expipe saved as 148-300921-3 instead, deleting the curation I'd already completed for that recording?

Processing 148-300921-2

Cleaning up existing NWB file
Removing LFP
Removing RawUnits-kilosort2

Preprocessing recording:
Num channels: 32
Duration: 612.59 s
Detected bad channels: ['CH4' 'CH30' 'CH57' 'CH59' 'CH60']
Active channels: 27
Saving preprocessed recording

Spike sorting with kilosort2 using installed sorter
Usage: which [options] [--] COMMAND [...]
Write the full path of COMMAND(s) to standard output.

--version, -[vV] Print version and exit successfully.
--help, Print this help and exit successfully.
--skip-dot Skip directories in PATH that start with a dot.
--skip-tilde Skip directories in PATH that start with a tilde.
--show-dot Don't expand a dot to current directory in output.
--show-tilde Output a tilde for HOME directory for non-root.
--tty-only Stop processing options on the right if not on tty.
--all, -a Print all matches in PATH, not just the first
--read-alias, -i Read list of aliases from stdin.
--skip-alias Ignore option --read-alias; don't read stdin.
--read-functions Read shell functions from stdin.
--skip-functions Ignore option --read-functions; don't read stdin.

Recommended use is to write the output of (alias; declare -f) to standard
input, so that which can show aliases and shell functions. See which(1) for
examples.

If the options --read-alias and/or --read-functions are specified then the
output can be a full alias or function definition, optionally followed by
the full path of each command used inside of those.

Report bugs to which-bugs@gnu.org.
Found 45 units!

Postprocessing
Extracting waveforms
Computing QC metrics
Exporting to phy
Generating sortingview link
https://figurl.org/f?v=npm://@fi-sci/figurl-sortingview@12/dist&d=sha1://aa2aeba2fb5fd03ec745d59a11dc5d79e9911247&label=**148-300921-2**-kilosort2

Writing to NWB
Adding units table
Adding LFP
Cleaning up
Saved to NWB: /projects/ec109/maria/novel-env-nwb/actions/148-300921-3/data/main.nwb
Total processing time: 516.0s

[alejoe91]

Oh that doesn't sound right! I'll take a look. Maybe the reference to the new action was held somewhere..

[alejoe91]

So the nwb_file_path is retrieved from the action metadata: https://github.com/CINPLA/expipe-plugin-cinpla/blob/dev/src/expipe_plugin_cinpla/scripts/process.py#L56

Then it is not updated anywhere in the function. Not sure how this has happened