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

#  Turn on command line echo
set -x

#  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

#  Copy needed datasets
cp -r ~/allpaths/* .

#  ulimit (stack) is needed by the allpaths program
ulimit -s 100000

#  prepare data for allpaths:
mkdir -p test.genome/data
PrepareAllPathsInputs.pl\
 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

# Assemble data:
RunAllPathsLG \
 PRE=$PWD\
 REFERENCE_NAME=test.genome\
 DATA_SUBDIR=data\
 RUN=run\
 SUBDIR=test\
 TARGETS=standard\
 THREADS=16\
 OVERWRITE=True\
 | tee -a assemble.out

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

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