#!/bin/bash
#SBATCH -t 12:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE
./single_job

module load QIIME2/2019.7

qiime diversity core-metrics-phylogenetic \
  --i-phylogeny /data/mramseylab/raw_reads/2018_Serum/Runcomb/rooted-tree-Run3.qza \
  --i-table  /data/mramseylab/proc_reads/filtered/Run3-Mock-table.qza \
  --p-sampling-depth 55682 \
  --m-metadata-file /data/mramseylab/metadata/Serum2.tsv \
  --output-dir /data/mramseylab/proc_reads/filtered/core-metrics-results-Run3-Mock

qiime diversity alpha-group-significance \
  --i-alpha-diversity /data/mramseylab/proc_reads/filtered/core-metrics-results-Run3-Mock/faith_pd_vector.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum2.tsv \
  --o-visualization /data/mramseylab/proc_reads/filtered/core-metrics-results-Run3-Mock/faith-pd-group-significance.qzv

qiime diversity beta-group-significance \
  --i-distance-matrix /data/mramseylab/proc_reads/filtered/core-metrics-results-Run3-Mock/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file  /data/mramseylab/metadata/Serum2.tsv \
  --m-metadata-column Condition \
  --o-visualization /data/mramseylab/proc_reads/filtered/core-metrics-results-Run3-Mock/unweighted-unifrac-Condition-significance.qzv \