#!/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/FS5BS5
clsdir=/data/mramseylab/16S/classifiers/homd-classifier/taxonomy.qza
visdir=/data/mramseylab/16S/visualizations/AL_2024/FSBS-filtered
metadir=/data/mramseylab/16S/metadata/meta_BSFS-2.tsv

qiime taxa collapse \
  --i-table $tabledir/filtered-reads.qza \
  --i-taxonomy $clsdir \
  --p-level 7 \
  --o-collapsed-table $tabledir/FSBS5-table.qza

qiime composition ancombc \
  --i-table $tabledir/FSBS5-table.qza \
  --m-metadata-file $metadir \
  --p-formula 'group' \
  --p-reference-levels 'group::FS5' \
  --o-differentials $tabledir/lvl7-ancombc-FSBS5-ref.qza

qiime composition da-barplot \
  --i-data $tabledir/lvl7-ancombc-FSBS5-ref.qza \
  --p-significance-threshold 0.05 \
  --p-level-delimiter ';' \
  --o-visualization $visdir/lvl7-da-barplot-05.qzv

qiime composition da-barplot \
  --i-data $tabledir/lvl7-ancombc-FSBS5-ref.qza \
  --p-significance-threshold 0.01 \
  --p-level-delimiter ';' \
  --o-visualization $visdir/lvl7-da-barplot-01.qzv


qiime composition da-barplot \
  --i-data $tabledir/lvl7-ancombc-FSBS5-ref.qza \
  --p-significance-threshold 0.001 \
  --p-level-delimiter ';' \
  --o-visualization $visdir/lvl7-da-barplot-001.qzv