Error when cleaning up metadata when using workdir in snakefile #2933
Description
Hello,
When I run a dryrun in snakemake, I get the following error:
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:
IMR90/assembly/verkko/assembly.haplotype1.fasta
IMR90/assembly/verkko/assembly.haplotype2.fasta
However, when I run:
snakemake --cleanup-metadata IMR90/assembly/verkko/assembly.haplotype1.fasta
I get the following error:
WorkflowError:
Failed to clean up metadata for the following files because the metadata was not present.
If this is expected, there is nothing to do.
Otherwise, the reason might be file system latency or still running jobs.
Consider running metadata cleanup again.
Files:
IMR90/assembly/verkko/assembly.haplotype1.fasta
I am wondering if this might be due to the "workdir:" that I have in my Snakefile?
I also tried to run --cleanup-metadata using the full path of the file, but I get the same WorkFlowError. I also tried running --cleanup-metadata in the working directory, but that also did not work.
Thanks for any assistance.
Snakemake version
8.14.0