#!/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 QIIME2/2024.2

tabledir=/data/mramseylab/16S/proc_reads/2024_AL_SUPP_6000/FST0
clsdir=/data/mramseylab/16S/classifiers/homd-classifier/taxonomy.qza
visdir=/data/mramseylab/16S/visualizations/AL_2024/FST0-filtered
metadir=/data/mramseylab/16S/metadata/FST0-test.tsv

qiime taxa collapse \
  --i-table $tabledir/FST0.qza \
  --i-taxonomy $clsdir \
  --p-level 6 \
  --o-collapsed-table $tabledir/FST0-table-TEST2.qza

qiime composition ancombc \
  --i-table $tabledir/FST0-table-TEST2.qza \
  --m-metadata-file $metadir \
  --p-formula 'media' \
  --p-reference-levels 'media::filtered' \
  --o-differentials $tabledir/l6-ancombc-FS-TEST-3.qza

qiime composition da-barplot \
  --i-data $tabledir/l6-ancombc-FS-TEST-3.qza \
  --p-significance-threshold 0.05 \
  --p-level-delimiter ';' \
  --o-visualization $visdir/l6-da-barplot-TEST3-05.qzv

qiime composition da-barplot \
  --i-data $tabledir/l6-ancombc-FS-TEST-3.qza \
  --p-significance-threshold 0.01 \
  --p-level-delimiter ';' \
  --o-visualization $visdir/l6-da-barplot-TEST3-01.qzv


qiime composition da-barplot \
  --i-data $tabledir/l6-ancombc-FS-TEST.qza \
  --p-significance-threshold 0.001 \
  --p-level-delimiter ';' \
  --o-visualization $visdir/l6-da-barplot-TEST-001.qzv