Basic Flags

These are the general flags that can be used during Configuration. These will be used via the command line (denoted CMD) or ini file (denoted INI).

-d / --database [string] [CMD]

  • Specify any number of FASTA formatted databases you would like to configure for EnTAP
  • Not necessary if you already have DIAMOND configured databases (.dmnd)

--out-dir [string] [CMD]

  • Specify an output directory for the databases to be sent to (recommended)
  • This will send the EnTAP database and DIAMOND databases to this location

-t / --threads [number] [CMD]

  • Specify thread number for Configuration

--data-generate [CMD]

  • Specify this flag is you would like to generate the EnTAP database rather than downloading from FTP (default)
  • I’d only use this if you’re having issues with the FTP

--data-type [flag] [INI]

  • Specify which databases you’d like to generate/download

      1. Binary Database (default) - This will be much quicker and is recommended
      1. SQL Database - Slower although will be more easily compatible with every system

  • This can be flagged multiple times (ex: - - data-type 0 - - data-type 1)

  • I would not use this flag unless you are experiencing issues with the EnTAP Binary Database