#!/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 1-1                           #-- 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]}


cat /srv/gsfs0/projects/snyder/hayanlee/projects/meta-gut/contigs/IDBA_UD/4021A/demux.4021A.rmbc.tl20.trim.clean.r1.fastq | grep -n 'COOPER:45:HCYNTBBXX:5:2206:26697:28411_125' 

cat /srv/gsfs0/projects/snyder/hayanlee/projects/meta-gut/contigs/IDBA_UD/4021A/demux.4021A.rmbc.tl25.trim.clean.r2.fastq | grep -n 'COOPER:45:HCYNTBBXX:5:2206:26697:28411_125'