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#PBS -l select=1:ncpus=1:mem=12gb
#PBS -l walltime=08:00:00

start=$SECONDS

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

bash ./ISA/bash/isa_pipeline.sh ./gps_run_data/gps ./gps_run_data/tn1207.fasta \
2000 gps_mega_run3 gps_mega ./ 500 ./act_compos_mega/ no /rds/general/project/bacterial_evo_genomics/live/gps_annotations_4_2_2020/strep_reference_fasta/strep_ref_database

duration=$(( SECONDS - start ))

echo $duration > mega_run_time.txt
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