#!/bin/bash
# Grid Engine options
#$ -N Trimming
#$ -l h_vmem=4G,h_rt=5:00:00 
#$ -pe mp 10
#$ -j y
#Standard report

echo "Path"
dir="/SCRATCH/cricasre/Metagen"
sequence=$dir/filter2
program=/home/cricasre/Genomica/WGS/Program

sample_seq=$(awk 'NR==n {print;exit}' n=$SGE_TASK_ID /home/cricasre/files/samples_trim.txt)
mkdir -p ${dir}/trimming
cd ${dir}/trimming

echo "Trimming low quality end reads and adapters"
echo ${sample_seq}

java -jar ${program}/trimmomatic-0.39.jar PE -threads 10 -phred33 -trimlog ${sample_seq} \
${sequence}/${sample_seq}_filter_R1.fastq.gz ${sequence}/${sample_seq}_filter_R2.fastq.gz \
-baseout ${sample_seq}.trim.fastq.gz \
ILLUMINACLIP:${program}/adapters/TruSeq3-PE-2.fa:2:30:10 \
LEADING:8 \
TRAILING:8 \
MINLEN:96 \
SLIDINGWINDOW:10:15

# CPU and RAM tracking
#JOB=$!
#./cpumemlog.sh $JOB
#cpumemlogplot.R cpumemlog.${JOB}.txt
echo "Termino el Programa"
# Standard report
echo
pwd
date