#!/bin/bash -l
#
#$ -cwd
#$ -j y
#$ -P waxmanlab
#$ -m be
#$ -M kkarri@bu.edu
#$ -N IntronicRef_for_TCPOAnalysis_v2
#$ -pe omp 16
#$ -l mem_per_core=8G
#$ -l h_rt=72:00:00
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
#old version used to run tabula muris data
#module load bcl2fastq/2.20
#module load cellranger/2.1.1

module load python2
module load bcl2fastq/2.20
module load cellranger/3.1.0

cellranger mkref --genome="IntronicRef_for_TCPOAnalysis_v2" --fasta="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/genome.fa" --genes="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/new_lncRNAs_reference/NewRefseqGTF/Intronic-ExonCollapsedGTF_forsnRNAseq_merged_correctedColec11_MtERCC_v2.gtf"

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