Description

From the MaxQuant home page: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. The search engine andromeda is integrated into MaxQuant as well as the viewer application for inspection of raw data and identification and quantification results.

Version

• 1.6.2.3

Authorized Users

• CIRCE account holders
• RRA account holders
• SC account holders

Platforms

• CIRCE cluster
• RRA cluster
• SC cluster

Modules

MaxQuant requires the following module file to run:

• apps/maxquant/1.6.2.3

• See Modules for more information.

Running MaxQuant on CIRCE/SC

The MaxQuant user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

• Note on CIRCE: Make sure to run your jobs from your $WORK directory!
• Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting a Job

Use a submit script like the following to run MaxQuant:

#!/bin/bash
#
#SBATCH --job-name=maxquant-test
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --mem-per-cpu=2048
#SBATCH --output=output.%j.maxquant-test
#SBATCH --time=01:00:00

#### SLURM single node test 
#### to run for 1 hour 
#### using 4 processor cores and 8 GB of memory

module purge
module add apps/maxquant/1.6.2.3

mono $MQHOME/bin/MaxQuantCmd.exe filename.xml

 

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./maxquant-test.sh

• You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

• MaxQuant Home Page
  • http://www.coxdocs.org/doku.php?id=maxquant:start
• MaxQuant User's Guide
  • http://www.coxdocs.org/doku.php?id=maxquant:manual:beginner

More Job Information

See the following for more detailed job submission information:

• SLURM User’s Guide
• Scheduling and Dispatch Policies
• Advanced Submit Techniques

Reporting Bugs

Report bugs with MaxQuant to the IT Help Desk: rc-help@usf.edu