#PBS -l select=1:ncpus=1:mem=2gb
#PBS -l walltime=00:31:00
#PBS -J 1-146

module load anaconda3/personal

source activate

conda activate tree_checker

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}missing_isolates.tsv"

Rscript --vanilla ../ISA/R/missing_isolate_checker.R $out_file

if [ -f $out_file ]
then 


cat $out_file >> ../tot_missing_isolates.tsv

fi