hzar.pbs

#!/bin/bash

#PBS -N hzar_BOX_rerun
#PBS -q q72h32c
#PBS -j oe
#PBS -o hzar_BOX_rerun.$PBS_JOBID
#PBS -m abe
#PBS -M btm002@email.uark.edu
#PBS -l nodes=1:ppn=32
#PBS -l walltime=72:00:00

module purge; module load mkl/18.0.1 R/3.4.3 parallel

cd $PBS_O_WORKDIR

LOCINAMES=BOX_HZAR_locinames.csv
NSAMPLES=BOX_HZAR_nsamples.csv
REFALLELE=FINAL_HZAR_DATA_refAlleles.csv
DIST=FIANL_HZAR_DATA_distances.csv
RSCRIPT=HZAR_runSingle.R
OUTDIR=rerun_output

mkdir -p /scratch/$PBS_JOBID/output

maxLocus=`awk -F"," '{print NF}' $LOCINAMES`

cp $LOCINAMES $NSAMPLES $REFALLELE $DIST $RSCRIPT /scratch/$PBS_JOBID/output
cd /scratch/$PBS_JOBID/output

parallel "Rscript --vanilla $RSCRIPT {} >loc{}.logfile.txt 2>&1" :::: <(seq 1 $maxLocus);

mkdir -p $PBS_O_WORKDIR/$OUTDIR

rsync -avh /scratch/$PBS_JOBID/output/* $PBS_O_WORKDIR/$OUTDIR