#!/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/16S/proc_reads/2022_AL_SUPP/2022/rooted-tree-2022-single.qza
procdir=/data/mramseylab/16S/proc_reads/2022_AL_SUPP/2022
metadir=/data/mramseylab/16S/metadata/plaque_meta_2.tsv
filtdir=/data/mramseylab/16S/proc_reads/2022_AL_SUPP/2022/filter-final-single.qza
cmr="sample-name"

qiime diversity core-metrics-phylogenetic \
--i-phylogeny $rawdir \
--i-table $filtdir \
--p-sampling-depth 5000 \
--m-metadata-file $metadir \
--output-dir $procdir$cmr

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

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

done