qsub_admixture_bot_mode_Garud2015_theta0_shortIntron

#$ -o output_error_directory       #-- output directory (fill in)
#$ -e output_error_directory       #-- error directory (fill in)
#$ -cwd                            #-- tell the job that it should start in your working directory
#$ -r y                            #-- tell the system that if a job crashes, it should be restarted
#$ -j y                            #-- tell the system that the STDERR and STDOUT should be joined
#$ -l h_data=1G                  #-- submits on nodes with enough free memory (required)
#$ -l h_rt=23:00:00               #-- runtime limit (see above; this requests 24 hours)
#$ -t 1-10                        #-- remove first '#' to specify the number of
#$ -m e                                   #-- tasks if desired (see Tips section)

. /u/local/Modules/default/init/modules.sh
module load python/2.7


# reset the mem to 1G
readarray is < ~/Jensen_response/tmp_intermediate_files/indexes.txt

is=(null ${is[@]}) # this pads the file with an extra line in the beginning. 
i=${is[$SGE_TASK_ID]}
echo $i


rho_in=5e-9  
adaptive_theta=0
selection=False    

locusLength=100 # will be replaced with short intron

model=admixture_bot_mode_Garud2015

file=/u/scratch/n/ngarud/tmp_intermediate_files/${model}_tmp_${i}.txt
outFile=~/Jensen_response/analysis/${model}_neutrality_shortIntron

bash ~/Jensen_response/scripts/run_any_model_short_Intron.sh ${model} ${file} $outFile $rho_in $adaptive_theta $selection $locusLength 

done