Starting analysis
If you’re running in a local configuration, you can start new analyses from within the MARTI GUI, or from the command line.
If you’re running in an HPC configuration, you must start analyses from the command line on your HPC system.
Starting MARTi from the command line
MARTi requires a configuration (or ‘config’) file in order to begin an analysis. This defines the input dataset, the analysis to be run and the options for the analysis.
To run a MARTi analysis:
marti -config <file> [options]
Where possible additional options include:
-options
to specify the location of a marti_engine_options.txt file to use instead of the files in the default locations.-queue
to set the default queue (partition) when using SLURM. Can also be set in config file.-dontcompressblast
will stop compression of BLAST files once parsed.-dontrunblast
will avoid re-running BLAST and will use the previously generated BLAST files.-dontrunnt
will avoid re-running BLAST nt and will use the previously generated BLAST files. BLAST processes other than ‘nt’ will still be run.
Creating a config file
To generate a new config file:
marti -writeconfig config.txt -rawdir /path/to/my/raw/data/dir -sampledir /path/to/sample/dir -runname MyRun -barcodes 1,2,3 -blast nt,card
Where:
-rawdir
specifies a path to a MinKNOW raw data directory (the directory containing fastq_pass directory or fastq directory for guppy run separately).-sampledir
specifies a path to a directory where MARTi will write intermediate and final files. If this doesn’t exist, it will be created.-runname
specifies the name of this run.-barcodes
specifies the barcodes being used, or can be left out if the run is not barcoded.-blast
provides a comma separated list of the BLAST processes to carry out.-centrifuge
provides a comma separated list of the Centrifuge processes to carry out.-kraken2
provides a comma separated list of the Kraken2 processes to carry out.
MARTi will generate a config file with default options and these can then be edited in a text editor.
Blast process configuration
The default options for blast processes are defined in the file marti_engine_options.txt which, by default, is found in the MARTi bin directory. Each blast process defined in this file has a name associated with it and this is the identifier to pass to the -blast option above. The options defined in this file will be the default ones written to the new config file.
MARTi looks for marti_engine_options.txt in three locations:
In the current directory.
If not in the current directory, in the user’s home directory (i.e. ~/marti_engine_options.txt).
If not in the user’s home directory, in the directory containing the MARTiEngine.jar, which unless you have changed things will be the bin directory.
Alternatively, you can specify the location of the file using the -options command line option. This is useful when running the docker image.