#PBS -q bl2x220g7q
#PBS -l select=1:ncpus=5:mem=10g
#PBS -l walltime=03:00:00
#PBS -l cput=30:00:00

source ~/programms/ame/bin/activate
WORK_DIR=~/loxP_project/2022-02-07_rings/
cd $WORK_DIR;
mkdir cutadapt;

for i in {65..96}
do
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o $WORK_DIR/cutadapt/cutIL_${i}_R1.fq.gz -p $WORK_DIR/cutadapt/cutIL_${i}_R2.fq.gz $WORK_DIR/raw/${i}_S${i}_L001_R1_001.fastq.gz $WORK_DIR/raw/${i}_S${i}_L001_R2_001.fastq.gz -m 8;
wait;
cutadapt -g ada1=AAACGAGTTTTAATGACTCCAACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA -y '{name}' -g ada2=ATGTCAGGAATTGTGAAAAAGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAACTGTA -y '{name}' -G ada1=AAACGAGTTTTAATGACTCCAACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA -y '{name}' -G ada2=ATGTCAGGAATTGTGAAAAAGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAACTGTA -y '{name}' -o $WORK_DIR/cutadapt/cut_barc_praimers_cutIL_${i}_R1.fq.gz -p $WORK_DIR/cutadapt/cut_barc_praimers_cutIL_${i}_R2.fq.gz $WORK_DIR/cutadapt/cutIL_${i}_R1.fq.gz $WORK_DIR/cutadapt/cutIL_${i}_R2.fq.gz --overlap 20;
done
