fetch

atb fetch

Download ATB parquet metadata tables

Synopsis

Download parquet metadata tables from AllTheBacteria.

By default the core tables are downloaded, which includes amrfinderplus.parquet. Note: AMR data is ~1.2 GB to download but expands to ~35 GB of per-genus indexes, so you'll be prompted to confirm before download and again before index build. Use --yes to skip both prompts and proceed automatically.

Use --all to download all available tables. Use --tables to specify exact tables by name.

atb fetch [flags]

Examples

  # Download core tables (includes AMR data)
  atb fetch

  # Download and build indexes automatically (no prompt)
  atb fetch --yes

  # Download all tables including ENA metadata
  atb fetch --all

  # Force re-download
  atb fetch --force

  # Download specific tables
  atb fetch --tables assembly.parquet,amrfinderplus.parquet

Options

      --all              download all available tables
      --force            re-download even if table already exists
  -h, --help             help for fetch
      --parallel int     parallel downloads (default from config)
      --tables strings   specific tables to download (comma-separated names)
  -y, --yes              build indexes without prompting

Options inherited from parent commands

      --config string     config file (default $HOME/.atb/config.toml)
      --data-dir string   directory for the local metadata index (default ~/.local/share/atb/data; override with $ATB_DATA_DIR)

SEE ALSO

• atb - Query and download AllTheBacteria genomes