#!/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

rawdir=/data/mramseylab/raw_reads/2023_AL_SUPP/triplicates/tripS/rooted-tree-pseudo-S.qza
filtdir=/data/mramseylab/raw_reads/2023_AL_SUPP/triplicates/tripS/S-saliva-table.qza
metadir=/data/mramseylab/16S/metadata/plaque_meta_S.tsv
visdir=/data/mramseylab/16S/visualizations/AL_2023/
cmr="master-core-metrics-results-SubjectS-Saliva-only-6000"

qiime diversity core-metrics-phylogenetic \
--i-phylogeny $rawdir \
--i-table $filtdir \
--p-sampling-depth 6000 \
--m-metadata-file $metadir \
--output-dir $visdir$cmr

qiime diversity alpha-group-significance \
--i-alpha-diversity $visdir$cmr/faith_pd_vector.qza \
--m-metadata-file $metadir \
--o-visualization $visdir$cmr/faith-pd-group-significance.qzv

qiime diversity alpha-group-significance \
--i-alpha-diversity $visdir$cmr/evenness_vector.qza \
--m-metadata-file $metadir \
--o-visualization $visdir$cmr/evenness-group-significance.qzv

array=( unweighted_unifrac_distance_matrix weighted_unifrac_distance_matrix bray_curtis_distance_matrix )

for i in "${array[@]}"
do

qiime diversity beta-group-significance \
--i-distance-matrix $visdir$cmr/$i.qza \
--m-metadata-file $metadir \
--m-metadata-column group \
--o-visualization $visdir$cmr/$i.qzv \
--p-pairwise

done