#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=48g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7

rawdir=/data/mramseylab/raw_reads/AL_v1v2_test
clsdir=/data/mramseylab/classifiers
metadata=/data/mramseylab/metadata/plaque_meta_3.5.tsv
procdir=/data/mramseylab/proc_reads/master-core-metrics-results-paired

#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-132-99-nb-classifier.qza \
  --i-reads $rawdir/rep-seqs-paired-v1v2.qza \
  --o-classification $clsdir/silva-taxonomy-AL/silva-taxonomy-AL-pairedv1v2.qza

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

qiime metadata tabulate \
  --m-input-file $clsdir/silva-taxonomy-AL/silva-taxonomy-AL-pairedv1v2.qza \
  --o-visualization $clsdir/silva-taxonomy-AL/silva-taxonomy-pairedv1v2.qzv

qiime taxa barplot \
  --i-table $procdir/rarefied_table.qza \
  --i-taxonomy $clsdir/silva-taxonomy-AL/silva-taxonomy-AL-pairedv1v2.qza \
  --m-metadata-file $metadata \
  --o-visualization $procdir/taxa-bar-plots-pairedv1v2.qzv

#added line of code above to take previously made rarefied table and info from silva-taxonomy/meta data file to give bar plots of taxonomic classification.