bug: jobs not finished in snakemake script (randomly, restart and they finish)

[berntpopp]

likely some random ressource problems

[berntpopp]

Status update (2026-02-13):

The Snakemake workflow exists in snakemake/plasmicheck.smk and appears functional. The random failures on restart are most likely caused by the race condition in create_indexes.py (#86) — when parallel Snakemake jobs try to create the same index simultaneously, they can corrupt files or fail intermittently.

Recommended fix path: Resolve #86 first (add file locking to create_indexes.py), then re-test Snakemake stability. If failures persist after that fix, this issue should be reopened with new diagnostics.