#!/bin/bash

#SBATCH --job-name=AMT1_Annotate     ## Name of the job.
#SBATCH -A AMARTINY_LAB     ## account to charge 
#SBATCH -p maxmem          ## partition/queue name
#SBATCH --nodes=1            ## (-N) number of nodes to use
#SBATCH --ntasks=1           ## (-n) number of tasks to launch
#SBATCH --cpus-per-task=1    ## number of cores the job needs
#SBATCH --error=ngless_err/%x-%J.err 
#SBATCH --output=ngless_err/%x-%J.err
#SBATCH -t 2-00:00:00         ## day run time limit
#SBATCH --mail-type=FAIL,END

# This script annotates a fasta file with non-redundant putative proteins (ORFs) using all 4 default MicrobeAnnotator databases and the DIAMOND search method

newgrp amartiny_lab 

# Activate conda environment

source ~/.bashrc

conda activate ngless

cd /pub/larkinsa/

ngless -j 1 --strict-threads --trace gmgc_annotate_amt.ngl 

## -t /pub/larkinsa/ngless-temp-out/ 

conda deactivate
