Fastfold AI Docs - Troubleshooting

Common Agent CLI issues and fixes for startup, keys, dependencies, and Windows installs.

If something fails, start with these common checks.

Symptom	Fix
`fastfold` fails at startup	`fastfold doctor`
Authentication failed (401 / invalid key)	Set a valid key: `fastfold config set llm.anthropic_api_key sk-ant-...` or run `fastfold setup`
Data not found	Check `fastfold data status`, then `fastfold data pull <dataset>` (or `fastfold data pull-all`)
Windows dependency issues	Use WSL2 + Ubuntu, or install `[win_build]`
Missing dependency	Reinstall with `uv tool install "fastfold-agent-cli[all]" --python 3.11`
Resume last session	`fastfold --continue`

Diagnostic commands

fastfold doctor
fastfold --version
fastfold setup