ule link_input fails sometimes

[cmkobel]

        
Touching output file output/220506_DnnT6S_carl/msfragger/link_input.done.
Traceback (most recent call last):
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/__init__.py", line 726, in snakemake
    success = workflow.execute(
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/workflow.py", line 1133, in execute
    raise e
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/workflow.py", line 1129, in execute
    success = self.scheduler.schedule()
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/scheduler.py", line 423, in schedule
    self._finish_jobs()
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/scheduler.py", line 526, in _finish_jobs
    self.get_executor(job).handle_job_success(job)
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/executors/__init__.py", line 633, in handle_job_success
    super().handle_job_success(job)
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/executors/__init__.py", line 232, in handle_job_success
    job.postprocess(
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/jobs.py", line 1076, in postprocess
    self.dag.check_and_touch_output(
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/dag.py", line 594, in check_and_touch_output
    f.touch()
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/io.py", line 707, in touch
    raise e
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/io.py", line 693, in touch
    with open(file, "w"):
PermissionError: [Errno 13] Permission denied: 'output/220506_DnnT6S_carl/msfragger/20220506_C9_Slot1-33_1_1971.d/.snakemake_timestamp'```

[cmkobel]

I have a strange feeling that the job graph is messing up by running individual jobs for each sample?

[cmkobel]

Probably not the problem since rule link_input is going to run once only, for twenty-something samples and an empty output directory.

[cmkobel]

Turned out it was not a bug.