Biowulf High Performance Computing at the NIH
pvactools on Biowulf

pVACtools is a cancer immunotherapy suite consisting of the following tools:

pVACseq
A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a list of tumor mutations.
pVACfuse
A tool for detecting neoantigens resulting from gene fusions.
pVACvector
A tool designed to aid specifically in the construction of DNA vector-based cancer vaccines.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[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 pvactools
[+] Loading pvactools 1.1.4

[user@cn3144 ~]$ allele="HLA-A*23:01,HLA-A*68:02,HLA-B*07:17,HLA-B*08:01,HLA-C*02:02,HLA-C*17:01"

[user@cn3144 ~]$ pvacseq run --iedb-install-directory /opt/iedb -e 8,9,10,11 --fasta-size=50 final.vcf Test ${allele} {NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign} outdir
Using TensorFlow backend.
Executing MHC Class I predictions
Converting .vcf to TSV
Completed
Splitting TSV into smaller chunks
Splitting TSV into smaller chunks - Entries 1-25
[...]
Splitting TSV into smaller chunks - Entries 226-230
Completed
Generating Variant Peptide FASTA and Key Files
Generating Variant Peptide FASTA and Key Files - Entries 1-50
[...]
Generating Variant Peptide FASTA and Key Files - Entries 451-460
Completed
Processing entries for Allele HLA-A*23:01 and Epitope Length 8 - Entries 1-50
Running IEDB on Allele HLA-A*23:01 and Epitope Length 8 with Method NetMHC - Entries 1-50
Completed
[...]
Processing entries for Allele HLA-C*17:01 and Epitope Length 11 - Entries 451-460
Allele HLA-C*17:01 not valid for Method NetMHC. Skipping.
Combining Parsed IEDB Output Files
Completed
Running Binding Filters
Completed
Running Coverage Filters
Completed
Running Transcript Support Level Filter
Complete
Running Top Score Filter
Completed
Creating Condensed Report
Completed
Ranking neoepitopes
Completed

Done: Pipeline finished successfully. File /spin1/users/user/pvacseq/outdir/MHC_Class_I/Test.filtered.condensed.ranked.tsv contains list of filtered putative neoantigens.

No MHC class II alleles chosen. Skipping MHC class II predictions.

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

Batch job
Most jobs should be run as batch jobs.

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

#! /bin/bash
# 
set -e

#!/bin/bash

cd /data/$USER/somedir

module load pvactools
allele="HLA-A*23:01,HLA-A*68:02,HLA-B*07:17,HLA-B*08:01,HLA-C*02:02,HLA-C*17:01"
pvacseq run --iedb-install-directory /opt/iedb -e 8,9,10,11 --fasta-size=50 final.vcf Test ${allele} \
    {NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign} outdir

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] pvactools.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

pvacseq run -e 11  --iedb-install-directory /opt/iedb out1.vcf Test1 HLA-C*07:02  \
       {NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign} out1
pvacseq run -e 11 --iedb-install-directory /opt/iedb  out2.vcf Test2 HLA-C*07:02  \
       {NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign} out2
[...]

Submit this job using the swarm command.

swarm -f pvactools.swarm [-g #]  --module pvactools
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module pvactools Loads the pvactools module for each subjob in the swarm