Directory cannot be locked

A previous run died without releasing its lock

why

Snakemake locks the working directory so two runs cannot corrupt each other's outputs. If a run is killed — Ctrl-C, a scheduler timeout, a dropped SSH session — the lock file survives it.

what to do

Confirm no other run is genuinely still going, then snakemake --unlock and start again. Only unlock when you are sure nothing else is running; unlocking a live run is how output actually gets corrupted.

Snakemake documented behaviour

This is one entry from BioErrors, a catalogue of bioinformatics error messages that point at the wrong thing. Every entry was traced to its real cause before it was written down.
If your error is not in it, paste it there and it gets traced and added.