Snakemake version
9.9.0
Describe the bug
I have a workflow that creates a directory with make_file, and then symlinks to that directory with rule link_to_D. Despite the input of link_to_D depending on the output directory of make_file, and the rules being run in the correct order, snakemake complains that the symlink directory "has older modification time (2025-07-30 18:34:17.469428) than input".
Logs
=> snakemake -c 1
Assuming unrestricted shared filesystem usage.
host: mymachine
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count
--------- -------
all 1
link_to_D 1
make_file 1
total 3
Select jobs to execute...
Execute 1 jobs...
[Thu Jul 31 13:33:09 2025]
localrule make_file:
output: dir1/D, dir1/D/file.txt
jobid: 2
reason: Missing output files: dir1/D
resources: tmpdir=/tmp
[Thu Jul 31 13:33:11 2025]
Finished jobid: 2 (Rule: make_file)
1 of 3 steps (33%) done
Select jobs to execute...
Execute 1 jobs...
[Thu Jul 31 13:33:11 2025]
localrule link_to_D:
input: dir1/D
output: dir2/D
jobid: 1
reason: Missing output files: dir2/D; Input files updated by another job: dir1/D
resources: tmpdir=/tmp
WorkflowError in rule link_to_D in file "/home/thekswenson/home/tmp/snakemake_test/Snakefile", line 19:
Output dir2/D has older modification time (2025-07-31 13:33:11.437842) than input dir1/D (2025-07-31 13:33:11.438434). This could indicate a clock skew problem in your network and would trigger a rerun of this job in the next execution and should therefore be fixed on system level. System time: 2025-07-31 13:33:11.439108 (rule link_to_D, line 33, /home/thekswenson/home/tmp/snakemake_test/Snakefile)
Exiting because a job execution failed. Look below for error messages
WorkflowError:
At least one job did not complete successfully.
Minimal example
import shutil
from pathlib import Path
rule all:
input:
'dir2/D'
rule make_file:
""" Touch a file. """
output:
directory('dir1/D'),
file='dir1/D/file.txt',
run:
Path(output.file).touch()
rule link_to_D:
""" Create a symlink to dir1/D in dir2. """
input:
'dir1/D'
output:
directory('dir2/D')
run:
Path(str(output)).symlink_to(f'{os.getcwd()}/{input}') Additional context
Snakemake version
9.9.0
Describe the bug
I have a workflow that creates a directory with
make_file, and then symlinks to that directory with rulelink_to_D. Despite the input oflink_to_Ddepending on the output directory ofmake_file, and the rules being run in the correct order, snakemake complains that the symlink directory "has older modification time (2025-07-30 18:34:17.469428) than input".Logs
Minimal example
Additional context