#!/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
echo "emails sent"
module load QIIME2/2024.2
echo "module loaded"

clsdir=/data/mramseylab/16S/classifiers/homd-classifier
samples=(BST0 BS5T0 FST0 FS5T0)

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

reads=/data/mramseylab/16S/proc_reads/2024_AL_SUPP_6000/"$i"/

if
qiime feature-classifier classify-sklearn \
  --i-classifier $clsdir/HOMD-classifier.qza \
  --i-reads $reads/filtered-reads.qza \
  --o-classification $reads/HOMD-"$i"taxa.qza; then
	echo "taxa aligned to classifier"
fi

if
qiime metadata tabulate \
  --m-input-file $reads/HOMD-"$i"taxa.qza \
  --o-visualization $reads/HOMD-"$i"taxa.qzv; then
	echo "metadata table made"
fi
fi
echo " Script DONE!!!!"

done