#!/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

rawdir=/data/mramseylab/raw_reads/2024_AL_SUPP
visdir=/data/mramseylab/16S/visualizations/AL_2024
metadata=/data/mramseylab/16S/metadata/meta_BSFS.tsv
clsdir=/data/mramseylab/16S/classifiers/homd-classifier

if qiime feature-table filter-samples \
  --i-table $rawdir/pseudo-denoise-table-2024.qza \
  --m-metadata-file $metadata \
  --p-where "[variable-type]='control' \ 
  --o-filtered-table $rawdir/BSFS-table.qza; then
  echo "samples filtered"
fi


if   qiime taxa collapse \
  --i-table $rawdir/BSFS-table.qza \
  --i-taxonomy $clsdir/taxonomy.qza \
  --p-level 6 \
  --o-collapsed-table $rawdir/BSFS-table-TEST.qza; then
  echo "taxa collpased"
fi

if qiime composition ancombc \
  --i-table $rawdir/BSFS-table-TEST.qza \
  --m-metadata-file $metadata \
  --p-formula 'medias' \
  --o-differentials $rawdir/TEST-media.qza; then
  echo "ancombc done"
fi

if qiime composition da-barplot \
  --i-data $rawdir/TEST-media.qza \
  --p-significance-threshold 0.001 \
  --p-level-delimiter ';' \
  --o-visualization $visdir/TEST-medias-lefse.qzv; then
  echo "visualization created"
fi