NetMHCpan predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks. From the website description:

The method is trained on a combination of more than 850,000 quantitative Binding Affinity (BA) and Mass-Spectrometry Eluted Ligands (EL) peptides. The BA data covers 170 MHC molecules from human (HLA-A, B, C, E), mouse (H-2), cattle (BoLA), primates (Patr, Mamu, Gogo), swine (SLA) and equine (Eqca). The EL data covers 177 MHC molecules from human (HLA-A, B, C, E), mouse (H-2), cattle (BoLA), primates (Patr, Mamu, Gogo), swine (SLA), equine (Eqca) and dog (DLA). Furthermore, the user can obtain predictions to any custom MHC class I molecule by uploading a full length MHC protein sequence. Predictions can be made for peptides of any length.

References:

• Birkir Reynisson, Bruno Alvarez, Sinu Paul, Bjoern Peters, Morten Nielsen. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 2020 Jul 2;48(W1):W449-W454.

• NetMHCpan Main Site

• Module Name: netmhcpan (see the modules page for more information)
• singlethreaded
• Example files in $NMTEST_DATA

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load netmhcpan

[user@cn3144 ~]$ cd /data/$USER

[user@cn3144 user]$ cp -r $NMTEST_DATA .

[user@cn3144 user]$ cd test

[user@cn3144 test]$ netMHCpan -p test.pep > test.pep.myout

[user@cn3144 test]$ netMHCpan -p test.pep -BA > test.pep_wBA.myout

[user@cn3144 test]$ netMHCpan test.fsa > test.fsa.myout

[user@cn3144 test]$ netMHCpan -hlaseq B0702.fsa -p test.pep > test.pep_userMHC.myout

[user@cn3144 test]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. netmhcpan.sh). For example:

#!/bin/bash
set -e
module load netmhcpan
cd /data/$USER/working
netMHCpan -p input.pep > input.pep.myout
netMHCpan -p input.pep -BA > input.pep_wBA.myout
netMHCpan -p input.fsa > input.fsa.myout
netMHCpan -hlaseq hla.fsa -p input.pep > output.pep_userMHC.myout

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] netmhcpan.sh

Create a swarmfile (e.g. netmhcpan.swarm). For example:

netMHCpan -hlaseq hla.fsa -p input1.pep > output1.pep_userMHC.myout
netMHCpan -hlaseq hla.fsa -p input2.pep > output2.pep_userMHC.myout
netMHCpan -hlaseq hla.fsa -p input3.pep > output3.pep_userMHC.myout
netMHCpan -hlaseq hla.fsa -p input4.pep > output4.pep_userMHC.myout

Submit this job using the swarm command.

swarm -f netmhcpan.swarm [-g #] -t 2 --module netmhcpan