#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=144g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

echo "Script started!"

module load QIIME2/2024.2

echo "module has loaded!"

if  qiime feature-classifier extract-reads \
    --i-sequences HOMD_16S_otu.qza \
    --p-f-primer AGAGTTTGATYMTGGCTCAG \
    --p-r-primer TGCTGCCTCCCGTAGRAGT \
    --p-trunc-len 311 \
    --p-min-length 100 \
    --p-max-length 400 \
    --o-reads ref-seq.qza; then
	echo "primer based classifier made!"
fi

 echo "Script completed successfully!"