Description

From the IEDB Analysis Resource web site: For users with batch processing needs, the MHC class I and II binding prediction tools are available as standalone scripts for download. These command line tools are kept in sync with the web tools and should therefore produce the same results as clicking through the web interface. The MHC_I binding tool contains a collection of peptide binding prediction methods for Major Histocompatibility Complex (MHC) class I molecules. This MHC class II binding affinity dataset consists of 44, 541 experimentally measured binging affinities covering 26 alleric variants. Two sets of randomly splitted 5-fold cross validation data are provided: the entire dataset ("ALL") and the similarity reduced dataset ("SR").

Version

• 2.7

Authorized Users

• CIRCE account holders
• SC account holders

Platforms

• CIRCE cluster
• RRA cluster
• SC cluster

Modules

• apps/mhc_i/2.17
• apps/mhc_ii/2.17.3

Running MHC on CIRCE/SC

The MHC 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.

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 30 minutes to run on a standard PC.

If, for example, you wish to use the NetMHCpan method to predict binding for a user defined MHC protein sequence and length 9 with protein sequence(s) in a file named input_sequence.fasta, you would set up a submit script to use samtools like this:

#!/bin/bash
#SBATCH --job-name=test_mhci 
#SBATCH --time=01:00:00 
#SBATCH -N 1 --ntasks-per-node=2 
#SBATCH --mem-per-cpu=4096
#SBATCH -o output.%j.%N.txt 
#SBATCH -e error.%j.%N.txt 

#### SLURM single node MHC I test 
#### to run for 2 hours 
#### using 2 processing cores and 8GB of memory

# Unload all modules, then load the mhc_i module:
module purge 
module load apps/mhc_i/2.17 

predict_binding.py netmhcpan \
  -m ./protein_mhc_B0702.fasta 9 ./input_sequence.fasta 

 
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 ./test_mhci.sh

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

Documentation

Home Page, User Guides, and Manuals

• MHC Home Page:
  • http://tools.immuneepitope.org/mhci/
• MHC User Guide:
  • /apps/mhc/mhc_i/2.17/README

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

• MHC Examples
  • /apps/mhc/mhc_i/2.17/examples

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 MHC to the IT Help Desk: rc-help@usf.edu