#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -P waxmanlab
#$ -m be
#$ -M kkarri@bu.edu
#$ -N dropseq_10X_G171C_lnconly_UseThis
#$ -pe omp 28
#$ -l mem_per_core=18G
#$ -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

module load bcl2fastq/2.20
module load cellranger/3.1.0


cellranger count --id="10X_G171C_pcgonly_UseThis" --transcriptome="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/mm10_premrna_v1.0_pcg-only"  --fastqs="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/H3LTJBBXX/10X_G171C_MissingLibrary_1_H3LTJBBXX" --sample="G171C"  --expect-cells=5000

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