$ snakemake --cleanup-metadata foobar.txt
Traceback (most recent call last):

  File "$HOME/.virtualenvs/test/lib/python3.12/site-packages/snakemake/cli.py", line 2128, in args_to_api
    dag_api.cleanup_metadata(args.cleanup_metadata)

  File "$HOME/.virtualenvs/test/lib/python3.12/site-packages/snakemake/api.py", line 604, in _handle_no_exec
    return method(self, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "$HOME/.virtualenvs/test/lib/python3.12/site-packages/snakemake/api.py", line 677, in cleanup_metadata
    self.workflow_api._workflow.cleanup_metadata(paths)

  File "$HOME/.virtualenvs/test/lib/python3.12/site-packages/snakemake/workflow.py", line 841, in cleanup_metadata
    success = self.persistence.cleanup_metadata(path)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "$HOME/.virtualenvs/test/lib/python3.12/site-packages/snakemake/persistence.py", line 228, in cleanup_metadata
    return self._delete_record(self._metadata_path, path)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "$HOME/.virtualenvs/test/lib/python3.12/site-packages/snakemake/persistence.py", line 644, in _delete_record
    recpath = self._record_path(subject, id)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "$HOME/.virtualenvs/test/lib/python3.12/site-packages/snakemake/persistence.py", line 702, in _record_path
    assert isinstance(id, _IOFile)
           ^^^^^^^^^^^^^^^^^^^^^^^

AssertionError

$ mkvirtualenv test
$ pip install snakemake
$ cat Snakefile 
rule foobar:
    input:
        "foo.txt",
        "bar.txt"
    output:
        "foobar.txt"
    shell:
        "sleep 100 && cat {input} > {output}"

$ snakemake
Assuming unrestricted shared filesystem usage.
host: pc1011901129
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Job stats:
job       count
------  -------
foobar        1
total         1

Select jobs to execute...
Execute 1 jobs...

[Fri Nov  8 10:46:59 2024]
localrule foobar:
    input: foo.txt, bar.txt
    output: foobar.txt
    jobid: 0
    reason: Missing output files: foobar.txt
    resources: tmpdir=/tmp

^CTerminating processes on user request, this might take some time.
[Fri Nov  8 10:47:00 2024]
Error in rule foobar:
    jobid: 0
    input: foo.txt, bar.txt
    output: foobar.txt
    shell:
        sleep 100 && cat foo.txt bar.txt > foobar.txt
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Complete log: .snakemake/log/2024-11-08T104659.843222.snakemake.log
WorkflowError:
At least one job did not complete successfully.

 $  cat foo.txt bar.txt > foobar.txt

$ snakemake
Assuming unrestricted shared filesystem usage.
host: pc1011901129
Building DAG of jobs...
IncompleteFilesException:
The files below seem to be incomplete. If you are sure that certain files are not incomplete, mark them as complete with

    snakemake --cleanup-metadata <filenames>

To re-generate the files rerun your command with the --rerun-incomplete flag.
Incomplete files:
foobar.txt

$ snakemake --cleanup-metadata foobar.txt