#PBS -l select=1:ncpus=1:mem=2gb #PBS -l walltime=01:00:00 #PBS -J 1-146 module load anaconda3/personal source activate conda activate insertion_site_analysis cd /rds/general/project/bacterial_evo_genomics/live/gps_annotations_4_2_2020/gps_gubbins_runs current_dir=$(head -n $PBS_ARRAY_INDEX dir_list.txt | tail -n 1) cd $current_dir out_prefix=$(echo $current_dir | grep -o -a gpsc\.[0-9]*_) out_file="${out_prefix}recombinations.csv" python ../ISA/python/embl_recombinations.py --embl_file *.recombination_predictions.embl \ --out_name $out_file cd ../ echo $out_prefix >> embl_recombinations_csv_finished.txt