#!/bin/sh

# SGI

#PBS -V
#PBS -N PristMITO2
#PBS -e PristMITO2.err
#PBS -o PristMITO2.out
#PBS -q high_mem 
#PBS -l place=scatter
#PBS -l select=1:ncpus=1:host=n010
#PBS -l walltime=100:00:00

# shm, sock, ssm, rdma, rdssm
FABRIC=rdma

CORES=$[ `cat $PBS_NODEFILE | wc -l` ]
NODES=$[ `uniq $PBS_NODEFILE | wc -l` ]

cd $PBS_O_WORKDIR

printf "Current time is: `date`\n";
printf "Current PBS work directory is: $PBS_O_WORKDIR\n";
printf "Current PBS queue is: $PBS_O_QUEUE\n";
printf "Current PBS job ID is: $PBS_JOBID\n";
printf "Current PBS job name is: $PBS_JOBNAME\n";
printf "PBS stdout log is: $PBS_O_WORKDIR/sgi_mpitest.err\n";
printf "PBS stderr log is: $PBS_O_WORKDIR/sgi_mpitest.log\n";
printf "Fabric interconnect selected is: $FABRIC\n";
printf "This jobs will run on $CORES processors.\n";

. /etc/profile.d/modules.sh

module load mpt && echo "Successfully load modules"

printf "mpiexec_mpt run command location is: `which mpiexec_mpt`\n";

TBEGIN=`echo "print time();" | perl`

printf "################################################\n";

/apps/MITObim.pl -start 1 -end 1000 -sample Pristimantis_sp -ref Rhyacotriton -readpool reads.fastq -maf Pristimantis_sp_mitGene_2_assembly/Pristimantis_sp_mitGene_2_d_results/Pristimantis_sp_mitGene_2_out.m
af --pair --readlength 150 --insert 300 --kbait 31 --clean --mirapath /apps/ &> MITObim.log

TEND=`echo "print time();" | perl`

printf "#################################################\n";
printf "+++ Job finished: `date`\n";
printf "+++ Job walltime: `expr $TEND - $TBEGIN`\n";
printf "#################################################\n";

/apps/MITObim.pl -start 1 -end 1000 -sample Pristimantis_sp -ref Rhyacotriton -readpool reads.fastq -maf Pristimantis_sp_mitGene_2_assembly/Pristimantis_sp_mitGene_2_d_results/Pristimantis_sp_mitGene_2_out.m
af --pair --readlength 150 --insert 300 --kbait 31 --clean --mirapath /apps/ &> MITObim.log

TEND=`echo "print time();" | perl`

printf "#################################################\n";
printf "+++ Job finished: `date`\n";
printf "+++ Job walltime: `expr $TEND - $TBEGIN`\n";
printf "#################################################\n";