Troubleshooting and FAQ

Common issues

  • Manifest paths incorrect: update absolute paths in your manifest files.
  • Docker runs out of memory: increase Docker memory to 8 GB+.
  • Deblur and sample names: avoid underscores; use alphanumerics, dashes, periods.
  • Long QZV loads (Empress): allow >10 minutes in browser.

Tips

  • Use Snakemake --printshellcmds and --dryrun to inspect planned execution.
  • Delete individual outputs to force regeneration, or target a file/rule directly.
  • To archive/compare runs, change run_name or copy output directories before re-running.

Performance

  • Set --cores according to machine capacity; certain steps parallelize well (e.g., taxonomy).
  • For large datasets, test truncation/trim parameters on a subset first.

Where to ask questions

  • Tourmaline GitHub issues: https://github.com/aomlomics/tourmaline/issues
  • Project wiki and README for additional examples.