#PBS -q dl560g10q@vm-pbs2
#PBS -l select=1:ncpus=5:mem=10g
#PBS -l walltime=01:00:00
#PBS -l cput=01:00:00

source ~/programms/ame/bin/activate
WORK_DIR=~/loxP_project/2022-06-14_rings/
cd $WORK_DIR;
mkdir cutadapt;
# Declare a string array with type
declare -a files=("undetermine")

for file in "${files[@]}"
do
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o $WORK_DIR/cutadapt/cutIL_${file}_R1.fq.gz -p $WORK_DIR/cutadapt/cutIL_${file}_R2.fq.gz $WORK_DIR/raw/${file}/${file}_R1_cutada2.fastq.gz $WORK_DIR/raw/${file}/${file}_R2_cutada2.fastq.gz -m 8;
wait;
cutadapt -g AAACGAGTTTTAATGACTCCAACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA -g ATGTCAGGAATTGTGAAAAAGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAACTGTA -G AAACGAGTTTTAATGACTCCAACTTAAGTGTATGTAAACTTCCGACTTCAACTGTA -G ATGTCAGGAATTGTGAAAAAGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAACTGTA -o $WORK_DIR/cutadapt/cut_barc_praimers_cutIL_${file}_R1.fq.gz -p $WORK_DIR/cutadapt/cut_barc_praimers_cutIL_${file}_R2.fq.gz $WORK_DIR/cutadapt/cutIL_${file}_R1.fq.gz $WORK_DIR/cutadapt/cutIL_${file}_R2.fq.gz --overlap 20;
done
