canu-hugemem.pbs

#!/bin/bash
#PBS -P xe2
#PBS -q normalbw
#PBS -l ncpus=28
#PBS -l walltime=24:00:00
#PBS -l other=gdata1
#PBS -l mem=250G
#PBS -l jobfs=400G
#PBS -l wd
#PBS -m abe
#PBS -M pbs@kdmurray.id.au


if [ "$SPECIES" == "" ]
then
    echo USAGE: $0 SPECIES
fi

module load gnuplot java/jdk1.8.0_60


set -euo pipefail # safe mode
set -x # logging


HERE=/g/data/xe2/projects/euc_pan_genome/
DIR=$HERE/workspaces/$SPECIES/canu-experimental
mkdir -p $DIR
cd $DIR

NEXT=$(qsub $HERE/scripts/canu-hugemem.pbs -v SPECIES="$SPECIES" -W depend=afterany:$PBS_JOBID )

/g/data/xe2/opt/tmp/canu/Linux-amd64/bin/canu                                  \
    -p $SPECIES                                                                \
    -d $DIR                                                                    \
    -correct                                                                   \
    -nanopore-raw $HERE/workspaces/$SPECIES/reads/${SPECIES}-qcd_main.fastq.gz \
    genomeSize=650m                                                            \
    useGrid=false                                                              \
    correctedErrorRate=0.2                                                     \
    maxThreads=28                                                              \
    maxMemory=250                                                              \
    stageDirectory="$PBS_JOBFS"                                                \
    java=$(which java)                                                         \
    gnuplot=$(which gnuplot)                                                   \
    > ${PBS_JOBID}_master.log  2>&1                                            \

qdel "$NEXT"