---
title: "Command Line Parameters"
canonical: "https://help.biobam.com/space/BCD/190185563/Command%20Line%20Parameters"
format: markdown
---
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 [http://geneontology.org/page/go-slim-and-subset-guide](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 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 ([ftp://ftp.expasy.org/databases/enzyme/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](ftp://ftp.expasy.org/databases/enzyme/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 [http://data.biobam.com/b2g_res/obo_files/go_latest.obo.gz](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).