#!/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

treedir=/data/mramseylab/raw_reads/2022_AL_SUPP/AL_2022
tabdir=/data/mramseylab/16S/proc_reads/2022_AL_SUPP/filteredsamples_2022_saliva
procdir=/data/mramseylab/proc_reads/al_2022_2/
metadir=/data/mramseylab/16S/metadata/plaque_meta_3.tsv
visdir=/data/mramseylab/16S/visualizations/AL_2022/
cmr="core-metrics-results-A-Saliva"

#for CMR make sure to NOT make the directory, code will do it itself

qiime diversity core-metrics-phylogenetic \
--i-phylogeny $treedir/rooted-tree-1.qza \
--i-table $tabdir/filtered_samples.qza \
--p-sampling-depth 2000 \
--m-metadata-file $metadir \
--output-dir $tabdir$cmr

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

qiime diversity alpha-group-significance \
--i-alpha-diversity $tabdir$cmr/evenness_vector.qza \
--m-metadata-file $metadir \
--o-visualization $tabdir$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 $tabdir$cmr/$i.qza \
--m-metadata-file $tabdir \
--m-metadata-column media-types \
--o-visualization $tabdir$cmr/$i.qzv \
--p-pairwise

done