#!/bin/bash
#$ -w e
#$ -cwd
#$ -now no
#$ -j yes
#$ -m eas
#$ -M accopeland@lbl.gov
#$ -l exclusive.c
#$ -pe pe_slots 16
#$ -l ram.c=13.5G
#$ -N run_bbqc.AAUAH
## -P prok-assembly.p
## -l h_rt=05:00:00

export OMP_NUM_THREADS=16

T=$(date "+%s")
OUT=$(hostname).${JOB_ID}.$T.stdout
ERR=$(hostname).${JOB_ID}.$T.stderr

function run_cmd() { 
	local RAM=$(free -b | awk '/Mem:/{print $4 * 0.85}') 
	local CMD="module load bbtools ; bbqc.sh in=AAUAH.8613.1.106099.GCCAA.anqdp.fastq.gz out=AAUAH.bbqc.fq.gz pigz unpigz ow=t fast=t "
	echo $CMD
	eval $CMD 2>>$ERR 1>>$OUT
}

run_cmd