#!/bin/bash -l
#$ -P my_project

# Specify hard time limit for the job. 
#   The job will be aborted if it runs longer than this time.
#   The default time is 12 hours
#$ -l h_rt=24:00:00

#$ -pe omp 8
##$ -l mem_per_core=8G


# Send an email when the job finishes or if it is aborted (by default no email is sent).
#$ -m ea

# Give job a name
#$ -N samtool_mergedbam

# Combine output and error files into a single file
#$ -j y

# Specify the output file name
#$ -o sam_merge.qlog

# Keep track of information related to the current job

#source ../G173_RNA/Scripts/00_Setup_Pipeline/01_Pipeline_Setup.sh


#OUTPUT_DIR='/restricted/projectnb/waxmanlab/tingyac/G170_173/'
#OUTPUT_DIR='/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/tingyac/G170_G173/'

cd $OUTPUT_DIR
echo "Hello"


source ~/.bashrc
module load samtools/1.10
module load bedtools/2.27.1


echo "=========================================================="
echo "Start date : $(date)"
echo "Job name : $JOB_NAME"
echo "Job ID : $JOB_ID"  "$SGE_TASK_ID"
echo "=========================================================="

samtools sort -T /tmp/ -o  merged_sorted.bam  merged_dual.bam
cp merged_sorted.bam .
##samtools sort merged_dual.bam 'merged_sorted'
#samtools index -bc merged_sorted.bam >merged_sorted.bam.bai