"Snakefile not found" when path contains a space, using run directive #3235
Description
Snakemake version
8.25.5
Describe the bug
Snakemake fails with "Snakefile /path/that/includes/a/space" (part after space truncated) not found.
Logs
$ snakemakeAssuming unrestricted shared filesystem usage.
host: ___________
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 16
Rules claiming more threads will be scaled down.
Job stats:
job count
------- -------
default 1
total 1
Select jobs to execute...
Execute 1 jobs...
[Thu Dec 19 11:54:53 2024]
localrule default:
jobid: 0
reason: Rules with neither input nor output files are always executed.
resources: tmpdir=/tmp
Error: Snakefile "/home/kyle/scratch/test-smk-bug/smk" not found.
[Thu Dec 19 11:54:55 2024]
Error in rule default:
jobid: 0
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-12-19T115453.901323.snakemake.log
WorkflowError:
At least one job did not complete successfully.
Minimal example
mkdir smk\ space\ bug && cd smk\ space\ bug
echo 'rule default:\n run:\n print("hello")' > Snakefile
snakemakeAdditional context
- The same thing happens in a symlinked folder to the folder with spaces in it
- The same thing happens in a subdirectory without spaces. i.e., a space anywhere in the path seems to break things
- It only happens when using the
rundirective, notshell - It doesn't happen with
--dry-run, but rather in the execution phase