pVACtools is a cancer immunotherapy suite consisting of the following tools:
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
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 ~]$
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
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 |