#!/bin/bash

#$ -N blast_prodigal           #-- set the name of the job; this will appear in the job listing
#$ -l h_vmem=300G                      #-- 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 1-19                           #-- specify the number of tasks 

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

/srv/gsfs0/projects/snyder/wenyu/usearch61 -usearch_global /srv/gsfs0/projects/snyder/wenyu/LongReads_10X/IDBA/prodigal_NT/${timept}.prodigal.fa -db ~/highres_microbiome_timecourse_analysis/novel_centroids/centroids_all_species.ffn -id 0.95 -strand both -alnout /srv/gsfs0/projects/snyder/ngarud/Usearch_BLAST_prodigal/${timept}_usearch_blast.txt


