Troubleshooting 🐞¶

This page lists common errors, their cause, and how to fix them.

Error message (excerpt)	Cause	Fix
`snakemake --dag failed`	Snakefile has syntax or missing files	Run Snakemake dry-run; fix rule definitions
`ERROR: Unsupported format`	wf2wf couldn’t auto-detect	Pass `--in-format` explicitly
`docker: command not found`	Docker not installed	Install Docker or use `--auto-env off`
`conda-lock not found`	Auto-env requested but binary missing	`pip install conda-lock` or `brew install conda-lock`
`push rejected: authentication required`	Registry push without login	`docker login <registry>` or use `--push-registry` with credentials
`Lost fields: retry` (during export)	Target engine can’t express feature	Accept loss or choose richer format; use `.loss.json` side-car
`JSON schema validation failed`	IR or CWL invalid	File a bug if produced by wf2wf, otherwise inspect paths in error

Verbosity flags¶

Add -v / --verbose to see stack traces and subprocess output. Combine with --debug for maximal logging.