#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