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.
pVACbind
A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a FASTA file.

References:

Documentation
Important Notes

The default module version as of March 2021 is 2.0 or greater. The newer versions break compatibility with previous versions. Please update your workflow or explicitly load older modules, for example module load pvactools/1.5.5

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 --gres=lscratch:5
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
/lscratch/46116226 exists
[+] Loading singularity  3.7.1  on cn3144
[+] Loading pvactools  2.0.1

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3144 ~]$ pvacseq download_example_data .

[user@cn3144 ~]$ pvacseq run \
> pvacseq_example_data/input.vcf \
> Test \
> HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
> MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
> pvacseq_example_output \
> -e1 8,9,10 \
> -e2 15
Executing MHC Class I predictions
Converting .vcf to TSV
Completed
Converting VCF to TSV
Completed
Generating Variant Peptide FASTA and Key File
Completed
Parsing the Variant Peptide FASTA and Key File
Completed
Calculating Manufacturability Metrics
Completed
Splitting TSV into smaller chunks
Splitting TSV into smaller chunks - Entries 1-24
Completed
Generating Variant Peptide FASTA and Key Files
Generating Variant Peptide FASTA and Key Files - Epitope Length 8 - Entries 1-48
Generating Variant Peptide FASTA and Key Files - Epitope Length 9 - Entries 1-48
Generating Variant Peptide FASTA and Key Files - Epitope Length 10 - Entries 1-48
Completed
[...]
Creating combined reports
Creating aggregated report
Completed
Running Binding Filters
Completed
Running Coverage Filters
Completed
Running Transcript Support Level Filter
Complete
Running Top Score Filter
Completed

Done: Pipeline finished successfully. File /lscratch/46116226//pvacseq_example_output/combined/Test.filtered.tsv contains list of filtered putative neoantigens

[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

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"
algorithms="MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign"
pvacseq run input.vcf \
        Test \
        $allele \
        $algorithms \
        output_dir \
        -e1 8,9,10 \
        -e2 15

Submit this job using the Slurm sbatch command.

sbatch [--mem=#G] [--time=##:##:##] [--gres=lscratch:#] 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 -e1 8,9,10 -e2 15 input1.vcf Test1 HLA-C*17:01 MHCflurry MHCnuggetsI MHCnuggetsII output1
pvacseq run -e1 8,9,10 -e2 15 input2.vcf Test2 HLA-C*17:01 MHCflurry MHCnuggetsI MHCnuggetsII output2
pvacseq run -e1 8,9,10 -e2 15 input3.vcf Test3 HLA-C*17:01 MHCflurry MHCnuggetsI MHCnuggetsII output3
pvacseq run -e1 8,9,10 -e2 15 input4.vcf Test4 HLA-C*17:01 MHCflurry MHCnuggetsI MHCnuggetsII output4

Submit this job using the swarm command.

swarm -f pvactools.swarm [-g #] --module pvactools --export=
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