Using the Command Line

Use the --help argument to get a list of arguments.

For example, on Windows:

CMD.exe --help

On Linux/OSX:

dotnet CMD.dll --help

The command-line arguments are:

-d - The protein databases (.fasta, .xml, .fasta.gz, .xml.gz file formats are supported)

-s - The spectra files (.mzML and .mgf are supported on Linux/OSX/Windows; Thermo .raw is supported on Windows)

-t - The task .toml files(i.e., a file containing MetaMorpheus's search settings)

-o - The output folder (optional; a folder will automatically be generated in your spectra file's directory with the date and time as the name)

-v - Runs a small test search using a database and yeast data file included with the MetaMorpheus installation (called the "microvignette")

-g - Generates default .toml files that you can modify. The output directory (-o) must be specified when using this parameter

The -d, -t and -s arguments are required.

Windows

To use MetaMorpheus command-line version, run the "CMD.exe" program with command-line arguments.

Preferably, when specifying a filepath, use the absolute file path inside of quotes.

Example:

CMD.exe -d "C:\MyFolder\myDatabase.fasta" -t "\home\myfolder\myTask1.toml" "\home\myfolder\myTask2.toml" -s "C:\MyFolder\mySpectraFile.mzML"

Linux

MetaMorpheus is best run in Linux via .NET Core. The current MetaMorpheus version requires .NET Core 2.1. You can also use Mono, though historically there have been RAM issues.

You can run the .NET Core version of MetaMorpheus with the "dotnet CMD.dll" command. You will likely not be able to open Thermo .raw files in Linux; you should convert them to .mzML before searching with MetaMorpheus.

Example:

dotnet CMD.dll -d "\home\myfolder\mydatabase.fasta" -t "\home\myfolder\myTask1.toml" "\home\myfolder\myTask2.toml" -s "\home\mySpectraFile.mzML"