Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing,
communications and data analytics.

#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=10:00
#PBS -o allpaths.out
#PBS -j oe
#PBS -q debug
#

#  Change to scratch directory
cd $SCRATCH
pwd
#  Turn on Job Accounting
ja
#  Set up the  module command (used below) 
source /usr/share/modules/init/bash
# Load allpaths-lg module to make allpaths executables availiable
module load allpaths-lg
# turn on command line echo
set -x # Copy needed datasets cp -r ~/allpaths/* . # ulimit (stack) is needed by the allpaths program ulimit -s 100000 # prepare data for allpaths:
# set HOSTS to one less than ncpus value mkdir -p test.genome/data PrepareAllPathsInputs.pl\
HOSTS=15\ DATA_DIR=$PWD/test.genome/data\ PLOIDY=1\ IN_GROUPS_CSV=in_groups.csv\ IN_LIBS_CSV=in_libs.csv\ GENOME_SIZE=200000\ OVERWRITE=True\ | tee prepare.out

# Stop Job Accounting; Print a usage report: ja -chlst

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