#!/bin/bash -l

# Set SCC project
#$ -P waxmanlab

# 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=48:00:00

# 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 cuffmerge_18-8-19

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

# Specify the output file name
#$ -o cuffmerge_18-8-19_v2.qlog

#$ -pe omp 8
# Keep track of information related to the current job
echo "=========================================================="
echo "Start date : $(date)"
echo "Job name : $JOB_NAME"
echo "Job ID : $JOB_ID"  "$SGE_TASK_ID"
echo "=========================================================="

source ~/.bashrc

module load boost/1.69.0
module load samtools/1.9
module load bowtie2/2.3.4.1
module load cufflinks/2.2.1
module load python2/2.7.16
cuffmerge -o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new -g /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genes.gtf -s /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genomeWithRandom.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/assemblies.txt