#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE
#SBATCH --mail-user=mramsey@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7

rawdir=/data/mramseylab/raw_reads/2018_Serum/Merge_runs/
clsdir=/data/mramseylab/classifiers/

#for the silva release 132 99 .fna file

qiime feature-classifier classify-sklearn \
  --i-classifier $clsdir\gg-13-8-99-nb-classifier.qza \
  --i-reads $rawdir\rep-seqs-merge.qza \
  --o-classification $clsdir\gg-taxonomy.qza

#output the taxonomy table to check for A. baumanii strains in it afterwards. 

qiime metadata tabulate \
  --m-input-file $clsdir\gg-taxonomy.qza \
  --o-visualization $clsdir\gg-taxonomy.qzv