---

name: inference-cli description: "Run OmegaFold CLI inference from FASTA to PDB safely, including devices, weights, resources, dry-run validation, and troubleshooting." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

OmegaFold inference CLI

Use this sub-skill when a task needs to run or validate OmegaFold command-line inference from a FASTA file to PDB outputs. Prefer the installed omegafold console script; use the installed-package fallback python -m omegafold only when the console script is unavailable but the package import works.

Fast path

1. Validate the CLI without downloading model weights:

   python scripts/omegafold_cli_smoke.py
   

2. Inspect a FASTA and print a planned command without running inference:

   python scripts/omegafold_cli_smoke.py --fasta INPUT_FILE.fasta --output-dir OUTPUT_DIRECTORY --model 2 --device cuda
   

3. Run full inference only when weights, device, memory, and runtime are acceptable:

   omegafold INPUT_FILE.fasta OUTPUT_DIRECTORY --model 1 --device cuda
   

Route by need

• Use CLI reference for flags, defaults, model choices, command templates, and installed-module fallback syntax.
• Use inference workflow for safe validation, weights/cache decisions, device/resource planning, and output expectations.
• Use troubleshooting for install/import errors, Python and Torch compatibility, missing weights, device mismatch, OOM, and output mistakes.
• Use scripts/omegafold_cli_smoke.py for no-download CLI help checks and FASTA dry-run planning.
• For FASTA normalization details, output file naming, PDB confidence fields, and validation of generated structures, route to data-and-outputs.
• For direct Python use of OmegaFold, make_config, fasta2inputs, and tensor contracts, route to model-api.

Safety defaults

• omegafold --help is safe: it prints parser help and does not load weights.
• omegafold INPUT_FILE.fasta OUTPUT_DIRECTORY ... is not a smoke test: argument parsing selects a model, may download weights, then loads a large torch checkpoint before inference.
• Avoid full inference unless the user has approved network/download cost or has provided a local --weights_file, and the selected --device has enough memory.