#!/bin/bash -l
#$ -cwd
#$ -j y
#$ -P wax-dk
#$ -o log.txt
#$ -N task
#$ -pe omp 8
#$ -l mem_per_core=8G
#$ -l h_rt=06:00:00
# -l scratch_free=200G


echo "=========================================================="
Start_Time=$(date +"%s")
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 "=========================================================="

set -eu

zcat G190G193_normalized_atac_fragments.tsv.gz | rg -v "JH|GL|chrM|random"  > tmpfile
cat tmpfile | cut -d"-" -f2 | cut -f1,2 | sort | uniq -c > stats.txt
## stats.txt number of hits, sample_id, number of duplicates/umis???

End_Time=$(date +"%s")
diff=$(($End_Time-$Start_Time))
echo "$(($diff / 3600)) hours, $((($diff / 60) % 60)) minutes and $(($diff % 60)) seconds elapsed."
echo "=========================================================="