#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -P waxmanlab
#$ -m be
#$ -M kkarri@bu.edu
#$ -N grep_GSE77729_R2_PB
#$ -pe omp 8
#$ -l mem_per_core=1G
#$ -l h_rt=24:00:00
echo "=========================================================="
echo "Starting on       : $(date)"
echo "Running on node   : $(hostname)"
echo "Current job ID    : $JOB_ID"
echo "Current job name  : $JOB_NAME"
echo "Task index number : $TASK_ID"
echo "=========================================================="

source ~/.bashrc

# Submit an array job with 3 tasks 
#$ -t 1-4

# Use the SGE_TASK_ID environment variable to select the appropriate input file from bash array
# Bash array index starts from 0, so we need to subtract one from SGE_TASK_ID value
inputs=(SRR3157440 SRR3157441 SRR3157442)
index=$(($SGE_TASK_ID-1))
taskinput=${inputs[$index]}

grep -E '@SRR*.*/2$' "$taskinput".fastq -A 3 > "$taskinput"_R2.fastq



echo "Finished  .............. $(date)"