#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=2 --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/2023_SUPP_V1V2
clsdir=/data/mramseylab/classifiers
metadata=/data/mramseylab/metadata/plaque_meta_5.tsv
visdir=/data/mramseylab/visualizations/AL_2023
procdir=/data/mramseylab/proc_reads/2023_Master/core-metric-results

qiime taxa barplot \
  --i-table $procdir/rarefied_table.qza \
  --i-taxonomy $clsdir/silva-taxonomy-AL2023/silva-mod-2023-paired.qza \
  --m-metadata-file $metadata \
  --o-visualization $visdir/filtered-taxa-bar-mod-paired-v1v2.qzv

qiime metadata tabulate \
  --m-input-file $clsdir/silva-taxonomy-AL2023/silva-mod-2023-paired.qza \
  --o-visualization $visdir/silva-mod-2023-paired.qzv