Command Line Parameters

This section gives a quick guide on the parameters used in Blast2GO CLI. Some command examples will be given in the end of the detailed description.

Load or import data commands:

  • loadfasta <path> Path to fasta file. Activate -protein option when working with amino acids.
  • loadblast <path> Load Blast .xml results (pre 2.2.31) -outfmt 5
  • loadblast31 <path> Load Blast .xml/.json/.zip results (2.2.31+) -outfmt 13/14/15/16
  • loadips48 <path> Load InterProScan 4.8 data file or folder
  • loadips50 <path> Load InterProScan 5.0+ data file or folder
  • loadannot <path> Load a .annot file
  • loadb2g <path> Load a Blast2GO .b2g file
  • loadbox <path> Load an OmicsBox .box file

Analysis commands:

  • mapping Run the Gene Ontology mapping.
  • annotation Run the Blast2GO Annotation algorithm.
  • ecmapping Map Annotated GOs to their Enzyme Codes (Included when -annotation is set)
  • goslim <path> Run goslim using an *.obo file. Possible subset obo files can either be downloaded from, or customized by hand with OBO-Edit2.
  • cloudblast <cloudkey> Run CloudBlast via webservice. This requires a working internet connection and a valid CloudBlast key with a positive balance.
  • cloudunitbalance <cloudkey> Print the BioBam Bioninformatics Cloud computation unit balance. This requires a working internet connection.
  • extractfasta <path> Extract features from a fasta reference to a fasta file (path). Needs configuration in the properties file.
  • ips <email> Run InterPro via webservice. This requires a working internet connection, a valid email address and that your data-set contains sequence data.
  • cloudips <cloudkey> Run InterPro for your nucleotide or amino acid sequences via the BioBam Bioinformatics Cloud Platform. This requires a working internet connection and a valid Cloud key with a positive balance.
  • localblast <path> Run Blast ver. 2.4.0+ against a local database. Necessary Blast binaries will be downloaded to the indicated folder, if not provided. It is necessary is a correctly configured local blast database (properties file).

Save or export commands:

  • saveannot <path> Save the functional annotations (Gene Ontology terms and Enzymes) as .annot
  • savebox <path> Save the project as .box
  • savelog <path> Save the log to a specified file.
  • savelorf <path> Convert nucleotide sequences (FASTA format) into amino acid sequences (longest Open Reading Frame, FASTA format). This function may be used to prepare a FASTA file for a local InterProScan run.
  • savereport <path> Create .pdf report
  • saveseqtable <path> Save your data as it would be shown in OmicsBox (tab-separated)
  • statistics <charts> Provide a comma-separated list of desired statistical charts (-statistics without options to get a list of all available charts). ’-statistics all’ will try to export all statistics that are available. The option -nameprefix will be ignored.
  • exportgeneric <path> Export sequence data in tabular format for post processing

Other Options:

  • createproperties <path> The default properties file will be created here.
  • createkeyfile Create a file which contains a unique ID for your computer. This file is nessesary to issue license keys.
  • enzymedat <path> Provide a specific version of enzyme.dat (
  • enzclass <path> Provide a specific version of enzclass.txt (
  • help Display this message
  • nameprefix <name> Prefix for any output filenames in case you do not specifiy a path (default: b2g_project)
  • properties <path> Properties file (mandatory)
  • showlicenseinfo Show details about the currently available license.
  • tempfolder <path> Temporary folder (default: System temp folder)
  • useobo <path> The obo file to use for annotation, some statistics and various file im- and exports. Download the latest version from
  • workspace <path> Workspace folder, e.g. where the results will be saved if not specified (default: current folder)

If a path is specified for a save option (e.g. -saveannot), the options workstation and nameprefix will be ignored for this particular option (see Use Case Examples for detailed information).