#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -P waxmanlab
#$ -m be
#$ -M kkarri@bu.edu
#$ -o Citeseq_G172.log
#$ -N Citeseq_G172
#$ -pe omp 16
#$ -l mem_per_core=4G
#$ -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


echo "Copy"

CITE-seq-Count -R1 "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/HASH_Citeseq/Hashtag_R1.fastq.gz" -R2 "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/HASH_Citeseq/Hashtag_R2.fastq.gz"  -t "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/HASH_Citeseq/hash.csv" -cbf 1 -cbl 16 -umif 17 -umil 28 -cells 40000 -o "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/HASH_Citeseq"

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