#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=288g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2023.7

rawdir=/data/mramseylab/raw_reads/2024_AL_SUPP
clsdir=/data/mramseylab/16S/classifiers
visdir=/data/mramseylab/16S/visualizations/AL_2024

#for the silva release 132 99 .fna file
#file is present and already converted to .qza for this version of silva

qiime feature-classifier classify-sklearn \
  --i-classifier $clsdir/silva-138-99-nb-classifier.qza \
  --i-reads $rawdir/pseudo-rep-seqs-v1v2-2024.qza \
  --o-classification $clsdir/silva-taxonomy-test-2024.qza

  qiime metadata tabulate \
  --m-input-file $clsdir/silva-taxonomy-test-2024.qza \
  --o-visualization $visdir/taxonomy-ID-test.qzv

#output the taxonomy table to check for classification/contamination strains afterwards.