#!/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 QIIME2/2019.7

raw=/data/mramseylab/raw_reads/tripA
metaf=/data/mramseylab/raw_reads/tripA/core-metric-results-A/bray_curtis_distance_matrix.qza
metadir=/data/mramseylab/metadata/plaque_meta_A.tsv

qiime longitudinal first-distances \
  --i-distance-matrix $metaf \
  --m-metadata-file $metadir \
  --p-state-column media \
  --p-individual-id-column subject \
  --p-replicate-handling random \
  --o-first-distances $raw/first-distances.qza

  qiime longitudinal volatility \
  --m-metadata-file $metadir \
  --m-metadata-file $raw/first-distances.qza \
  --p-default-metric Distance \
  --p-default-group-column timepoint \
  --p-state-column media \
  --p-individual-id-column subject \
  --o-visualization $raw/volatility.qzv