Difference between revisions of "Parabricks"

Latest revision as of 21:25, 14 December 2022

Description

Parabricks is a software suite for genomic analysis. It delivers major improvements in throughput time for common analytical tasks in genomics, including germline and somatic analysis. The core of the Parabricks software is its data pipeline which takes raw data and transforms it according to the user's requirements.

Parabricks makes both GPU-accelerated pipelines and some standalone tools available.

Environment Modules

Run module spider parabricks to find out what environment modules are available for this application.

System Variables

HPC_PARABRICKS_DIR - installation directory
HPC_PARABRICKS_BIN - executable directory

Additional Information

An example job resource request based on the Nvidia recommendation:

srun -p hpg-ai -N 1 --cpus-per-task=16 --gpus=a100:2 --mem=32gb --time=200:00 --pty bash -i

Prabricks requires 2 to 8 A100 GPUs to run. The '--num-gpus X' pbrun argument must match the number 'X' of requested GPUs. If not specified parabricks will try to run on all gpus on the compute node and exit with an error.

Note that a parabricks run may produce an error if the paths used as arguments for the run resolve to symlinks. Containerized tools need real paths i.e. use the /blue/mygroup/myuser/project/inputdir path instead of a shorter ~/blue/project/inputdir path that's using a symlink even if the ~/blue symlink is pointing to the /blue/mygroup/myuser/ directory./

Job Script Examples

Expand to view script sample.

#!/bin/bash
#SBATCH --partition=hpg-ai               # partition
#SBATCH --time=4:00:00              # wall time
#SBATCH --mem=64gb              # all mem avail
#SBATCH --mail-type=FAIL        # only send email on failure
#SBATCH --mail-user=your@email.com
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --gpus=a100:2  # Number A100 GPUs, 2-8
#SBATCH --output=pb_%j.log
date;hostname;pwd

# Load the Parabricks environment module
module load parabricks

# Set data directories
DATA_DIR="/blue/nvidia-parabricks/g.burnett/parabricks_sample"
SAMPLE_1="${DATA_DIR}/Data/sample_1.fq.gz"
SAMPLE_2="${DATA_DIR}/Data/sample_2.fq.gz"
REF="${DATA_DIR}/Ref/Homo_sapiens_assembly38.fasta"
OUTPUT_DIR="${DATA_DIR}"

# Make the output directory
mkdir -p ${OUTPUT_DIR}

# Run germline
pbrun germline \
        --ref ${REF} \
        --in-fq ${SAMPLE_1} ${SAMPLE_2} \
        --out-bam ${OUTPUT_DIR}/germline.bam \
	--out-variants ${OUTPUT_DIR}/germline.vcf |& tee ${OUTPUT_DIR}/germline.log

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]]
+[[Category:Software]][[Category:Phylogenetics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|parabricks}}
@@ Line 6: / Line 6: @@
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
 |{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
-|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
+|{{#vardefine:job|1}}            <!--JOB SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
 |{{#vardefine:testing|}}       <!--PROFILING-->
@@ Line 38: / Line 38: @@
 An example job resource request based on the Nvidia recommendation:
-  srun -p gpu --constraint=rtx6000 -N 1 --cpus-per-task=16 --gpus=1 --mem=32gb --time=200:00 --pty bash -i
+  srun -p hpg-ai -N 1 --cpus-per-task=16 --gpus=a100:2 --mem=32gb --time=200:00 --pty bash -i
-It is recommended to use the RTX6000 GPUs because the RTX 2080ti cards do no have enough memory. The '--num-gpus X' pbrun argument must match the number 'X' of requested GPUs. If not specified parabricks will try to run on all gpus on the compute node and exit with an error.
+Prabricks requires 2 to 8 A100 GPUs to run. The '--num-gpus X' pbrun argument must match the number 'X' of requested GPUs. If not specified parabricks will try to run on all gpus on the compute node and exit with an error.
 Note that a parabricks run may produce an error if the paths used as arguments for the run resolve to symlinks. Containerized tools need real paths i.e. use the /blue/mygroup/myuser/project/inputdir path instead of a shorter ~/blue/project/inputdir path that's using a symlink even if the ~/blue symlink is pointing to the /blue/mygroup/myuser/ directory./
@@ Line 47: / Line 47: @@
 <!--Job Scripts-->
 {{#if: {{#var: job}}|==Job Script Examples==
-See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
+<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
+''Expand to view script sample.''
+<div class="mw-collapsible-content" style="padding: 5px;">
+<pre>
+#!/bin/bash
+#SBATCH --partition=hpg-ai               # partition
+#SBATCH --time=4:00:00              # wall time
+#SBATCH --mem=64gb              # all mem avail
+#SBATCH --mail-type=FAIL        # only send email on failure
+#SBATCH --mail-user=your@email.com
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=8
+#SBATCH --gpus=a100:2  # Number A100 GPUs, 2-8
+#SBATCH --output=pb_%j.log
+date;hostname;pwd
+# Load the Parabricks environment module
+module load parabricks
+# Set data directories
+DATA_DIR="/blue/nvidia-parabricks/g.burnett/parabricks_sample"
+SAMPLE_1="${DATA_DIR}/Data/sample_1.fq.gz"
+SAMPLE_2="${DATA_DIR}/Data/sample_2.fq.gz"
+REF="${DATA_DIR}/Ref/Homo_sapiens_assembly38.fasta"
+OUTPUT_DIR="${DATA_DIR}"
+# Make the output directory
+mkdir -p ${OUTPUT_DIR}
+# Run germline
+pbrun germline \
+        --ref ${REF} \
+        --in-fq ${SAMPLE_1} ${SAMPLE_2} \
+        --out-bam ${OUTPUT_DIR}/germline.bam \
+	--out-variants ${OUTPUT_DIR}/germline.vcf |& tee ${OUTPUT_DIR}/germline.log
+</pre>
+</div>
+</div>
 |}}
 <!--Policy-->