main.nwb deleted after failed spikesorting

[mariapfj]

when running spikesorting (kilosort2) on recording /maria/mec-social-nwb/actions/145-151021-5, I got the following error message (under). After this, the original main.nwb file is deleted and I have to re-register the recording. This has happened once or twice before, but I didn't connect the missing nwb file with the previous failed spikesorting until now. However, if I remember correctly I am usually able to re-register and spikesort without issue, so it doesn't seem to be an issue with the data or an issue that can easily be recreated. For that reason this is mainly a PSA unless the issue can be identified from the following error alone?

Processing 145-151021-5
N JOBS 24

Cleaning up existing NWB file

Preprocessing recording:
Num channels: 32
Duration: 949.27 s
Detected bad channels: ['CH7' 'CH8']
Active channels: 30
Saving preprocessed recording

Spike sorting with kilosort2 using installed sorter
Usage: /usr/bin/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 114 units!
Removed 0 units with less than 3 spikes

Postprocessing
Computing extensions
Computing QC metrics
Exporting to phy

Writing to NWB
Error exporting to NWB: [Errno 2] Unable to synchronously open file (unable to open file: name = '/projects/ec109/maria/mec-social-nwb/actions/145-151021-5/data/main_tmp.nwb', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
ERROR: unable to process 145-151021-5
Traceback (most recent call last):
File "/fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/scripts/process.py", line 311, in process_ecephys
with NWBHDF5IO(nwb_path_tmp, mode="r") as read_io:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/site-packages/hdmf/utils.py", line 668, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/site-packages/pynwb/init.py", line 406, in init
super().load_namespaces(tm, path, file=file_obj, driver=driver, aws_region=aws_region)
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/site-packages/hdmf/utils.py", line 668, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/site-packages/hdmf/backends/hdf5/h5tools.py", line 185, in load_namespaces
open_file_obj = cls.__resolve_file_obj(path, file_obj, driver, aws_region=aws_region)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/site-packages/hdmf/backends/hdf5/h5tools.py", line 158, in __resolve_file_obj
file_obj = File(path, 'r', **file_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fp/homes01/u01/ec-mariapfj/.local/lib/python3.11/site-packages/h5py/_hl/files.py", line 562, in init
fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fp/homes01/u01/ec-mariapfj/.local/lib/python3.11/site-packages/h5py/_hl/files.py", line 235, in make_fid
fid = h5f.open(name, flags, fapl=fapl)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5f.pyx", line 102, in h5py.h5f.open
FileNotFoundError: [Errno 2] Unable to synchronously open file (unable to open file: name = '/projects/ec109/maria/mec-social-nwb/actions/145-151021-5/data/main_tmp.nwb', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/widgets/process.py", line 300, in on_run
process.process_ecephys(
File "/fp/projects01/ec109/software/expipe-plugin-cinpla/src/expipe_plugin_cinpla/scripts/process.py", line 362, in process_ecephys
shutil.copy(nwb_path_tmp, nwb_path)
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/shutil.py", line 431, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/projects/ec109/conda-envs/cinpla/lib/python3.11/shutil.py", line 256, in copyfile
with open(src, 'rb') as fsrc:
^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/projects/ec109/maria/mec-social-nwb/actions/145-151021-5/data/main_tmp.nwb'