#!/bin/bash
#SBATCH -t 4:00:00
#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_2.tsv
visdir=/data/mramseylab/visualizations/
filtdir=/data/mramseylab/proc_reads/
fil=fil-media


mkdir $filtdir$fil

qiime feature-table filter-samples \
  --i-table $tablein \
  --m-metadata-file $metadir \
  --p-where "[media-types] IN ('mucin','in vivo','Saliva','Glucose')AND NOT [environmental-setting]=('polystyrene')
" \
  --o-filtered-table  $filtdir$fil/table-filtered_media.qza

done