Running Magnum

Starting Magnum

Magnum is run from a command line. For simplicity, only a single argument is required, the name of the configuration file. Details for setting your configuration file and the parameters contained within can be found from their respective links. The recommended way to operate Magnum is to store the data and configuration file in a convenient directory, navigate to it, then execute the Magnum application with the configuration file:

$ cd projects/data_set1
$ /usr/bin/magnum data_set1.conf

In the above example, you would substitute your own data directories, configuration file, and path to Magnum with the appropriate names and locations for your installation.

Helpful Hint

Microsoft Windows users may have difficulty finding their command line prompt. It can be quickly accessed from the Start Menu by typing "cmd" in the menu search box. Once open, it operates similarly to a Unix/Linux prompt (or perhaps more accurately, a DOS prompt).

During Execution

The first statement you should see printed to the screen is the version, date, and source information for Magnum:

Magnum version 1.0.0, February 10 2021
Copyright Michael Hoopmann, Institute for Systems Biology

This information is important as Magnum is in continuous development and different versions may produce different results. It is recommended that you use the latest version of Magnum, but it may be helpful to also maintain legacy versions so that results may be replicated at a later date. Additionally, the version number is printed inside the Magnum results for your reference.

Analysis progress is reported during execution. The following stages are reported to the user:

  • Database parsing - number of proteins and peptides to be searched.
  • Spectra reading - number of spectra to be analyzed.
  • Preprocessing - precursor mapping, etc.
  • Spectral analysis
  • E-value calculation and exporting results

The time at the completion of analysis is reported last and the command prompt is returned to the user.

Post Execution

After completion of the algorithm, several files will be exported to the storage device. Unless otherwise specified in the configuration file, exported files will be in the current working directory that you navigated to prior to starting Magnum.

All exported results are in text and/or XML format. The basic set of Magnum results is provided in the file set by the output_file parameter. An additional set of files containing the same results, but formatted for use with Percolator, were exported with the base name set from the percolator_file parameter.

Additional details describing these file formats and using them in downstream analysis can be found on the blank and Validating PSMs pages.