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bqsr_apply_run_parallel.pbs
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bqsr_apply_run_parallel.pbs
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#!/bin/bash
##########################################################################
#
# Platform: NCI Gadi HPC
# Usage: qsub bqsr_apply_run_parallel.pbs
# Version: 2.0
#
# For more details see: https://github.com/Sydney-Informatics-Hub/Fastq-to-BAM
#
# If you use this script towards a publication, please acknowledge the
# Sydney Informatics Hub (or co-authorship, where appropriate).
#
# Suggested acknowledgement:
# The authors acknowledge the support provided by the Sydney Informatics Hub,
# a Core Research Facility of the University of Sydney. This research/project
# was undertaken with the assistance of resources and services from the National
# Computational Infrastructure (NCI), which is supported by the Australian
# Government, and the Australian BioCommons which is enabled by NCRIS via
# Bioplatforms Australia funding.
#
##########################################################################
#PBS -P
#PBS -N bqsr_apply
#PBS -l walltime=00:00:00
#PBS -l ncpus=
#PBS -l mem=GB
#PBS -W umask=022
#PBS -q normal
#PBS -l wd
#PBS -o ./Logs/bqsr_apply.o
#PBS -e ./Logs/bqsr_apply.e
#PBS -lstorage=
set -e
INPUTS=./Inputs/bqsr_apply.inputs
NCPUS=2 #single threaded, but needed for mem
mkdir -p ../BQSR_apply ./Logs/BQSR_apply ./Logs/BQSR_apply_error_capture
#########################################################
# Do not edit below this line
#########################################################
module load nci-parallel/1.0.0a
module load openmpi/4.1.0
module load gatk/4.1.8.1 #loads also java/jdk1.8.0_60
module load samtools/1.10
# SCRIPT
SCRIPT=./bqsr_apply.sh
M=$(( PBS_NCI_NCPUS_PER_NODE / NCPUS )) #tasks per node
sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
--map-by node:PE=${NCPUS} \
nci-parallel \
--verbose \
--input-file ${PBS_JOBFS}/input-file