#!/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

treein=/data/mramseylab/raw_reads/2024_AL_SUPP/rooted-tree-pseudo-v1v2-2024.qza
tabledir=/data/mramseylab/16S/proc_reads/2024_AL_SUPP_6000/filteredsamples_2024/filtered_samples.qza
metadir=/data/mramseylab/16S/metadata/meta_BSFS.tsv
filtdir=/data/mramseylab/16S/proc_reads/2024_AL_SUPP_6000/filteredsamples_2024-2
SAMDEPTH=6000

if qiime diversity core-metrics-phylogenetic \
--i-phylogeny $treein \
--i-table $tabledir \
--p-sampling-depth $SAMDEPTH \
--m-metadata-file $metadir \
--output-dir $filtdir; then
echo "core metrics created"
fi

if qiime diversity alpha \
--i-table $tabledir \
--p-metric chao1 \
--o-alpha-diversity $filtdir/chao1_vector.qza; then
echo "chao metric made"
fi 

if qiime diversity alpha-group-significance \
--i-alpha-diversity $filtdir/chao1_vector.qza \
--m-metadata-file $metadir \
--o-visualization $filtdir/chao1_group-significance.qzv; then
echo "chao vector calced"
fi

if qiime diversity alpha-group-significance \
--i-alpha-diversity $filtdir/faith_pd_vector.qza \
--m-metadata-file $metadir \
--o-visualization $filtdir/filtered_faith-pd-group-significance.qzv; then
echo "faith pd calcd"
fi

if qiime diversity alpha-group-significance \
--i-alpha-diversity $filtdir/evenness_vector.qza \
--m-metadata-file $metadir \
--o-visualization $filtdir/filtered_evenness-group-significance.qzv; then
echo "eveness calc"
fi 

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 $filtdir/$i.qza \
--m-metadata-file $metadir \
--m-metadata-column group \
--o-visualization $filtdir/$i.qzv \
--p-pairwise

done