#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=mramsey@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7

tablein=/data/mramseylab/raw_reads/2018_Serum/Merge_runs/denoise-table-merge.qza
clsdir=/data/mramseylab/classifiers/
metadir=/data/mramseylab/metadata/
visdir=/data/mramseylab/visualizations/
# filter status of input files, "initial" is the 1st pass no filter at all
fil=-initial

array=( silva-taxonomy silva-mod-taxonomy gg-taxonomy )

for i in "${array[@]}"
do

qiime taxa barplot \
  --i-table $tablein \
  --i-taxonomy $clsdir$i.qza \
  --m-metadata-file $metadir\Serum4.tsv \
  --o-visualization $visdir$fil$i\.qzv

done