#!/bin/bash

#$ -N MIDAS_species_rerun        #-- set the name of the job; this will appear in the job listing
#$ -l h_vmem=2G                      #-- set the maximum memory usage (per slot). on scg3 the default is 1GB of h_vmem per slot
#$ -l h_rt=168:00:00                 #-- set the maximum run time, hh:mm:ss, default is 6hrs on scg3
#$ -w e                              #-- check for errors in the job submission options
#$ -j y                              #-- join the stdout and stderr streams into one file
#$ -o ~/output_error_directory       #-- output directory 
#$ -e ~/output_error_directory       #-- error directory   
#$ -t 1-5                           #-- specify the number of tasks 

readarray files < ~/snyder_project/timepts_rerun_species.txt
files=(null ${files[@]}) # this pads the file with an extra line in the beginning.
timept=${files[$SGE_TASK_ID]}

module load python/2.7.9 

export PYTHONPATH=$PYTHONPATH:/home/ngarud/snyder_project/software/MIDAS
export PATH=$PATH:/home/ngarud/snyder_project/software/MIDAS/scripts
export MIDAS_DB=/home/ngarud/snyder_project/software/midas_db_v1.2


echo $timept

OUTDIR=/srv/gsfs0/scratch/ngarud/snyder_project/MIDAS_output/${timept}
mkdir $OUTDIR
indir=/srv/gsfs0/projects/snyder/hayanlee/projects/meta-gut/contigs/IDBA_UD


echo 'species'
run_midas.py species $OUTDIR -1 $indir/${timept}/demux.${timept}.rmbc.tl20.trim.clean.r1.fastq -2 $indir/${timept}/demux.${timept}.rmbc.tl25.trim.clean.r2.fastq

