#!/bin/bash
#SBATCH -t 8:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7

tablein=/data/mramseylab/raw_reads/AL_2022/denoise-table-1.qza
clsdir=/data/mramseylab/classifiers/
metadir=/data/mramseylab/metadata/plaque_meta_1.tsv
visdir=/data/mramseylab/visualizations/
filtdir=/data/mramseylab/proc_reads/


fil=metadata-filter-AL


mkdir $filtdir$fil

qiime feature-table filter-samples \
--i-table $tablein \
--m-metadata-file $metadir \
--p-where "[environmental-setting]='hydroxyapatite disc'" \
--o-filtered-table  $filtdir$fil/control-fil-table.qza

qiime taxa collapse \
--control-table $filtdir$fil/control-fil-table.qza \
--i-taxonomy $clsdir\silva-mod-taxonomy.qza \
--p-level 6 \
--o-collapsed-table $filtdir$fil/control-fil-collapse-table.qza