parabricks: a software suite for performing secondary analysis of NGS DNA and RNA data

Quick Links

The Clara Parabricks toolkit is a set of GPU-accelerated genome analysis tools for secondary analysis of next generation sequencing data. It includes GPU-accelerated tools for preprocessing, QC, alignment, variant calling, and GVCF processing.

References:

Mohammed Alser, Zülal Bingöl, et al. Accelerating Genome Analysis: A Primer on an Ongoing Journey. IEEE Micro, Volume: 40, Issue: 5, 2020.
Karl R Franke, Erin L Crowgey. Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms. Genomics & Informatics, Volume 18(1), 2020.

Documentation

Parabricks 4.0.0 documentation

Important Notes

Module Name: parabricks (see the modules page for more information)
Parabricks requires a GPU with at least CUDA architecture 60. Currently, on the cluster this means a V100, V100x, or A100 gpu. You can select from these by specifying --gres=gpu:1 and --constraint="gpua100|gpuv100|gpuv100x".
Monitor your memory utilization with the HPC Dashboard. Running low on memory may cause unpredictable slowdowns in Parabricks software.
Running out of GPU memory may cause an error like: cudaSafeCall() failed at ParaBricks/src/samGenerator.cu/772: out of memory

Some Parabricks programs include a --low-memory option that may help with this

All tools in Parabricks are used the the pbrun command line tool.
Unusual environment variables set
- PARABRICKS_TEST_DATA: Parabricks sample data

Interactive job

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

[user@biowulf]$ sinteractive --gres=lscratch:40,gpu:1 \
                    --mem=32g \
                    -c16 \
                    --constraint="gpua100|gpuv100|gpuv100x"

[user@cn4464 ~]$ module load parabricks  
[+] Loading parabricks  4.0.0  on cn4464
[+] Loading singularity  3.8.5-1  on cn4464

[user@cn4464 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn4464 ~]$ tar xf $PARABRICKS_TEST_DATA

[user@cn4464 ~]$ pbrun --help
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation

usage: pbrun  []
Help: pbrun -h

command can be a TOOL or FULL PIPELINE. Example:
pbrun fq2bam --ref genome.fa --in-fq sample_1.fq.gz sample_2.fq.gz --out-bam sample.bam
pbrun germline --ref genome.fa --in-fq sample_1.fq.gz sample_2.fq.gz --out-bam sample.bam --out-variants sample.vcf

command options for standalone TOOL
applybqsr               - Apply BQSR report to a BAM file and generate a new BAM file
bam2fq                  - Convert a BAM file to FASTQ
bammetrics              - Collect WGS Metrics on a BAM file
bamsort                 - Sort a BAM file
bqsr                    - Collect BQSR report on a BAM file
collectmultiplemetrics  - Collect multiple classes of metrics on a BAM file
dbsnp                   - Annotate variants based on a dbsnp
deepvariant             - Run GPU-DeepVariant for calling germline variants
fq2bam                  - Run bwa mem, co-ordinate sorting, marking duplicates, and Base Quality Score Recalibration
genotypegvcf            - Convert a GVCF to VCF
haplotypecaller         - Run GPU-HaplotypeCaller for calling germline variants
indexgvcf               - Index a GVCF file
mutectcaller            - Run GPU-Mutect2 for tumor-normal analysis
postpon                 - Generate the final VCF output of doing mutect pon
prepon                  - Build an index for PON file, which is the prerequisite to performing mutect pon
rna_fq2bam              - Run RNA-seq data through the fq2bam pipeline
starfusion              - Identify candidate fusion transcripts supported by Illumina reads

command options for commonly used FULL PIPELINES
germline                - Run the germline pipeline from FASTQ to VCF
deepvariant_germline    - Run the germline pipeline from FASTQ to VCF using a deep neural network analysis
somatic                 - Run the somatic pipeline from FASTQ to VCF

Information about the software
version                 - Current version of Parabricks

Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation

positional arguments:
  command     The pipeline or tool to run.

optional arguments:
  -h, --help  show this help message and exit

# It may be necessary to add --low-memory on V100 nodes
[user@cn4464 ~]$ time pbrun fq2bam \
      --ref ./parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \
      --in-fq ./parabricks_sample/Data/sample_1.fq.gz ./parabricks_sample/Data/sample_2.fq.gz \
      --out-bam fq2bam_output.bam \
      --tmp-dir /lscratch/$SLURM_JOB_ID/tmp
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /lscratch/48192446/parabricks_sample/Data/sample_1.fq.gz and
/lscratch/48192446/parabricks_sample/Data/sample_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
[PB Info 2022-Sep-21 16:11:10] ------------------------------------------------------------------------------
[PB Info 2022-Sep-21 16:11:10] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2022-Sep-21 16:11:10] ||                              Version 4.0.0-1                             ||
[PB Info 2022-Sep-21 16:11:10] ||                       GPU-BWA mem, Sorting Phase-I                       ||
[PB Info 2022-Sep-21 16:11:10] ------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[PB Info 2022-Sep-21 16:11:31] GPU-BWA mem
[PB Info 2022-Sep-21 16:11:31] ProgressMeter    Reads           Base Pairs Aligned
[PB Info 2022-Sep-21 16:12:10] 5043564          580000000
[PB Info 2022-Sep-21 16:12:44] 10087128 1160000000
[PB Info 2022-Sep-21 16:13:16] 15130692 1740000000
[PB Info 2022-Sep-21 16:13:52] 20174256 2320000000
[PB Info 2022-Sep-21 16:14:24] 25217820 2900000000
[PB Info 2022-Sep-21 16:15:00] 30261384 3480000000
[PB Info 2022-Sep-21 16:15:35] 35304948 4060000000
[PB Info 2022-Sep-21 16:16:10] 40348512 4640000000
[PB Info 2022-Sep-21 16:16:43] 45392076 5220000000
[PB Info 2022-Sep-21 16:17:18] 50435640 5800000000
[PB Info 2022-Sep-21 16:17:39]
GPU-BWA Mem time: 368.713119 seconds
[PB Info 2022-Sep-21 16:17:39] GPU-BWA Mem is finished.


[main] CMD: /usr/local/parabricks/binaries//bin/bwa mem -Z ./pbOpts.txt /lscratch/48192446/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta /lscratch/48192446/parabricks_sample/Data/sample_1.fq.gz /lscratch/48192446/parabricks_sample/Data/sample_2.fq.gz @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
[main] Real time: 389.507 sec; CPU: 5828.472 sec
[PB Info 2022-Sep-21 16:17:39] ------------------------------------------------------------------------------
[PB Info 2022-Sep-21 16:17:39] ||        Program:                      GPU-BWA mem, Sorting Phase-I        ||
[PB Info 2022-Sep-21 16:17:39] ||        Version:                                           4.0.0-1        ||
[PB Info 2022-Sep-21 16:17:39] ||        Start Time:                       Wed Sep 21 16:11:10 2022        ||
[PB Info 2022-Sep-21 16:17:39] ||        End Time:                         Wed Sep 21 16:17:39 2022        ||
[PB Info 2022-Sep-21 16:17:39] ||        Total Time:                           6 minutes 29 seconds        ||
[PB Info 2022-Sep-21 16:17:39] ------------------------------------------------------------------------------
[PB Info 2022-Sep-21 16:17:42] ------------------------------------------------------------------------------
[PB Info 2022-Sep-21 16:17:42] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2022-Sep-21 16:17:42] ||                              Version 4.0.0-1                             ||
[PB Info 2022-Sep-21 16:17:42] ||                             Sorting Phase-II                             ||
[PB Info 2022-Sep-21 16:17:42] ------------------------------------------------------------------------------
[PB Info 2022-Sep-21 16:17:42] progressMeter - Percentage
[PB Info 2022-Sep-21 16:17:42] 0.0       0.00 GB
[PB Info 2022-Sep-21 16:17:52] 81.5      0.00 GB
[PB Info 2022-Sep-21 16:18:02] Sorting and Marking: 20.003 seconds
[PB Info 2022-Sep-21 16:18:02] ------------------------------------------------------------------------------
[PB Info 2022-Sep-21 16:18:02] ||        Program:                                  Sorting Phase-II        ||
[PB Info 2022-Sep-21 16:18:02] ||        Version:                                           4.0.0-1        ||
[PB Info 2022-Sep-21 16:18:02] ||        Start Time:                       Wed Sep 21 16:17:42 2022        ||
[PB Info 2022-Sep-21 16:18:02] ||        End Time:                         Wed Sep 21 16:18:02 2022        ||
[PB Info 2022-Sep-21 16:18:02] ||        Total Time:                                     20 seconds        ||
[PB Info 2022-Sep-21 16:18:02] ------------------------------------------------------------------------------
[PB Info 2022-Sep-21 16:18:02] ------------------------------------------------------------------------------
[PB Info 2022-Sep-21 16:18:02] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2022-Sep-21 16:18:02] ||                              Version 4.0.0-1                             ||
[PB Info 2022-Sep-21 16:18:02] ||                         Marking Duplicates, BQSR                         ||
[PB Info 2022-Sep-21 16:18:02] ------------------------------------------------------------------------------
[PB Info 2022-Sep-21 16:18:02] progressMeter -  Percentage
[PB Info 2022-Sep-21 16:18:12] 22.7      2.06 GB
[PB Info 2022-Sep-21 16:18:22] 44.1      2.16 GB
[PB Info 2022-Sep-21 16:18:32] 68.0      5.88 GB
[PB Info 2022-Sep-21 16:18:42] 96.0      0.20 GB
[PB Info 2022-Sep-21 16:18:52] 100.0     0.00 GB
[PB Info 2022-Sep-21 16:18:52] BQSR and writing final BAM:  50.370 seconds
[PB Info 2022-Sep-21 16:18:52] ------------------------------------------------------------------------------
[PB Info 2022-Sep-21 16:18:52] ||        Program:                          Marking Duplicates, BQSR        ||
[PB Info 2022-Sep-21 16:18:52] ||        Version:                                           4.0.0-1        ||
[PB Info 2022-Sep-21 16:18:52] ||        Start Time:                       Wed Sep 21 16:18:02 2022        ||
[PB Info 2022-Sep-21 16:18:52] ||        End Time:                         Wed Sep 21 16:18:52 2022        ||
[PB Info 2022-Sep-21 16:18:52] ||        Total Time:                                     50 seconds        ||
[PB Info 2022-Sep-21 16:18:52] ------------------------------------------------------------------------------

real    7m46.118s
user    107m4.313s
sys     2m16.551s

[user@cn4464 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226