Snakemake Unlock & Incomplete-Run Recovery

Pain point

Snakemake refuses to run because the working directory "cannot be locked," often after an interrupted run.

Repro/diagnostic steps

1. Capture the LockException message and working directory path.
2. Verify no other Snakemake process is running on the same target outputs.

Root causes (common)

• Stale lock files left after kill/power loss.
• Concurrent runs targeting overlapping outputs.

Fix workflow

1. Confirm no active Snakemake instance is running.
2. Use `--unlock` to remove stale locks.
3. Re-run with `--rerun-incomplete` if partial outputs exist.
4. Add guarded patterns to avoid two runs writing the same outputs.

Expected result

• Workflow resumes; incomplete outputs are rebuilt deterministically.

References

• https://stackoverflow.com/questions/59642199/how-can-i-run-multiple-runs-of-pipeline-with-different-config-files-issue-with
• https://github.com/snakemake/snakemake/blob/main/src/snakemake/exceptions.py