#!/bin/sh

# ACE

#################
# PBS VARIABLES #
#################

#PBS -V
#PBS -N abyss
#PBS -e pbs.err
#PBS -o pbs.out
#PBS -r n
##PBS -q <low_mem|mid|mem|high_mem|regular|workq>
#PBS -q high_mem
##PBS -l <free|pack|scatter|vscatter>
#PBS -l place=scatter
##PBS -l select=<1-12>:ncpus=<1-64>:mpiprocs=<1-64>:mem=<gb>:host=<n001-n012>
#PBS -l select=1:ncpus=64:mpiprocs=64:mem=512:host=n010
#PBS -l walltime=8760:00:00
# FABRIC=<shm|sock|ssm|rdma|rdssm>
FABRIC=rdma
CORES=$[ `cat $PBS_NODEFILE | wc -l` ]
NODES=$[ `uniq $PBS_NODEFILE | wc -l` ]
cd $PBS_O_WORKDIR

###################
# LOG AND MODULES #
###################

printf "Time =  `date`\n" > $PBS_JOBNAME.info
printf "PBS work directory = $PBS_O_WORKDIR\n" >> $PBS_JOBNAME.info
printf "PBS queue = $PBS_O_QUEUE\n" >> $PBS_JOBNAME.info
printf "PBS job ID = $PBS_JOBID\n" >> $PBS_JOBNAME.info
printf "PBS job name = $PBS_JOBNAME\n" >> $PBS_JOBNAME.info
printf "Fabric interconnect selected = $FABRIC\n" >> $PBS_JOBNAME.info
printf "This job will run on $CORES processors\n" >> $PBS_JOBNAME.info
printf "List of nodes in $PBS_NODEFILE\n\n" >> $PBS_JOBNAME.info
uniq $PBS_NODEFILE >> $PBS_JOBNAME.info
. /etc/profile.d/modules.sh
module load mpt && printf "\n\nSuccessfully load modules\n" >> $PBS_JOBNAME.info
printf "mpiexec_mpt run command location = `which mpiexec_mpt`\n" >> $PBS_JOBNAME.info
printf "\n[STAT] qstat -f $PBS_JOBID\n" >> $PBS_JOBNAME.info
qstat -f $PBS_JOBID >>  $PBS_JOBNAME.info
printf "\n[END] qstat -f $PBS_JOBID" >> $PBS_JOBNAME.info

###########
# COMMAND #
###########

#mpiexec_mpt -n $CORES <program/path> <arguments> <stderr> 2> <stdout>

# Export PATH to ABySS executables
export PATH=.:/apps:/apps/ABYSS:/apps/ABYSS/bin:$PATH

# Execute ABySS (abyss-pe)
/apps/ABYSS/bin/abyss-pe -C k21 np=64 j=64 k=21 n=10 N=10 name=sholk21 se='../se.fastq.gz' lib='pe1' pe1='../pe1.fastq.gz ../pe2.fastq.gz' mp='mp1' mp1='../mp1.fastq.gz ../mp2.fastq.gz' ABYSS_OPTIONS=--no-chastity 1>k21.out 2>k21.err

# /apps/ABYSS/bin/abyss-pe -C k21 np=64 j=64 k=21 n=10 N=10 name=Shol_k21 lib='pe' mp='mp' pe='../pe1.fastq.gz ../pe2.fastq.gz' mp='../mp1.fastq.gz ../mp2.fastq.gz' se='../se.fastq.gz' 1>k21.out 2>k21.err

# Execute ABySS for K-mers 21 to 63, with a step of 2
#export k
#for k in {21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63}; do
#    mkdir k21
#    mpiexec_mpt -n $CORES /apps/ABYSS/bin/abyss-pe -C k21 np=64 j=64 k=21 n=10 N=10 name=Shol_k21 lib='pe' mp='mp' pe='pe1.fastq.gz pe2.fastq.gz' mp='mp1.fastq.gz mp2.fastq.gz' se='se.fastq.gz' 1>k21.out 2>k21.err
#done

#/apps/ABYSS/bin/abyss-fac k*/Shol_k*-contigs.fa
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