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:

  • loadannot <path> Path to .annot file
  • loadb2g <path> Path to Blast2GO .b2g file
  • loadbox <path> Path to OmicsBox .box file
  • loadblast <path>Path to Blast .xml file (pre 2.2.31)
  • loadblast31 <path>Path to Blast .xml/.json/.zip file (2.2.31+)
  • loaddat <path> Path to Blast2GO .dat file (legacy format - use loadbox instead)
  • loadfasta <path> Path to fasta file. Activate -protein option when working with amino acids.
  • loadips48 <path> Path to InterProScan 4.8 file or folder
  • loadips50 <path> Path to InterProScan 5.0 file or folder

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 http://geneontology.org/page/go-slim-and-subset-guide, 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 against a local database. This requires a working internet connection in order to download the necessary Blast executable (Alternatively you can specify a binary folder manually and place the binary there). Also necessary is a correctly configured local blast database (properties file).

Save or export commands:

  • saveannot <path> Save the functional annotations (Gene Ontolgoy terms and Enzymes) as .annot
  • saveb2g <path> Save the project as .b2g
  • savebox <path> Save the project as .box
  • savedat <path> Save the project as .dat (legacy format - use saveb2g instead)
  • savelog <path> Save the log in 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 the Blast2GO GUI version (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> Path to where the default properties file should be created
  • createkeyfile Create a file which contains a unique ID for your computer. This file is nessesary to issue license keys.
  • enzyme <path> Provide a specific version of enzyme.dat (ftp://ftp.expasy.org/databases/enzyme/enzyme.dat).
  • enzclass <path> Provide a specific version of enzclass.txt (ftp://ftp.expasy.org/databases/enzyme/enzclass.txt).
  • help Display this message
  • nameprefix <name> Prefix for any output files, if you do not specify any path for them (default: b2g project)
  • properties <path> Path to properties file (mandatory)
  • protein Set this flag if the fasta file contains protein sequences. This option only makes sense together with the -loadfasta option.
  • showlicenseinfo Show details about the currently available license.
  • tempfolder <path> Path to temporary folder (default: Systems temp folder)
  • useobo <path> The obo file to use for annotation, some statistics and various file im- and exports. Download the latest version from http://data.biobam.com/b2g_res/obo_files/go_latest.obo.gz
  • 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).