Difference between revisions of "MaxQuant"
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''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. | ''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. | ||
{{AppStandardHeader| | {{AppStandardHeader|2.0.3.1|maxquant}} | ||
{{AppRunningOnAll}} | {{AppRunningOnAll}} | ||
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Once you get dropped into an interactive shell on the execution host, you need to load the MaxQuant module. | Once you get dropped into an interactive shell on the execution host, you need to load the MaxQuant module. | ||
<pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#000000; color:white;">[user@svc-3024-22-7 ~]$ module load apps/maxquant/ | <pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#000000; color:white;">[user@svc-3024-22-7 ~]$ module load apps/maxquant/2.0.3.1</pre> | ||
You should now be able to execute the GUI version (interactive mode) from the command line. | You should now be able to execute the GUI version (interactive mode) from the command line. | ||
<pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#000000; color:white;">[user@svc-3024-22-7 ~]$ mono $MQHOME/bin/MaxQuantGui.exe</pre> | <pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#000000; color:white;">[user@svc-3024-22-7 ~]$ mono $MQHOME/bin/MaxQuantGui.exe</pre> | ||
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# | # | ||
#SBATCH --job-name=maxquant-test | #SBATCH --job-name=maxquant-test | ||
#SBATCH -- | #SBATCH --ntasks=1 | ||
#SBATCH --mem-per-cpu=2048 | #SBATCH --mem-per-cpu=2048 | ||
#SBATCH --output=output.%j.maxquant-test | #SBATCH --output=output.%j.maxquant-test | ||
| Line 34: | Line 33: | ||
#### SLURM single node test | #### SLURM single node test | ||
#### to run for 1 hour | #### to run for 1 hour | ||
#### using | #### using 1 processor core and 8 GB of memory | ||
module purge | module purge | ||
module add apps/maxquant/ | module add apps/maxquant/2.0.3.1 | ||
mono $MQHOME/bin/MaxQuantCmd.exe filename.xml | mono $MQHOME/bin/MaxQuantCmd.exe filename.xml | ||
Revision as of 13:30, 7 April 2022
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
- 2.0.3.1
Authorized Users
CIRCEaccount holdersRRAaccount holdersSCaccount holders
Platforms
CIRCEclusterRRAclusterSCcluster
Modules
MaxQuant requires the following module file to run:
apps/maxquant/2.0.3.1
- 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 $WORK directory!
- Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
Interactive Mode
To run MaxQuant in an interactive session using the graphical interface, use srun to enter an interactive shell. This example is for 30 minutes using 1 cpu core:
[user@itn0 ~]$ srun --time=00:30:00 --ntasks=1 --pty /bin/bash
Once you get dropped into an interactive shell on the execution host, you need to load the MaxQuant module.
[user@svc-3024-22-7 ~]$ module load apps/maxquant/2.0.3.1
You should now be able to execute the GUI version (interactive mode) from the command line.
[user@svc-3024-22-7 ~]$ mono $MQHOME/bin/MaxQuantGui.exe
Submitting a Job
Use a submit script like the following to run MaxQuant:
#!/bin/bash # #SBATCH --job-name=maxquant-test #SBATCH --ntasks=1 #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 1 processor core and 8 GB of memory module purge module add apps/maxquant/2.0.3.1 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
- MaxQuant User's Guide
More Job Information
See the following for more detailed job submission information:
Reporting Bugs
Report bugs with MaxQuant to the IT Help Desk: rc-help@usf.edu