#!/bin/bash
#SBATCH -t 2:00:00
#SBATCH --mem=24g
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE
#SBATCH --mail-user=mramsey@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL
./Mock-2.sh

module load QIIME2/2019.7

qiime feature-table filter-samples \
  --i-table /data/mramseylab/Feb2020/postchimera/table.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum3.tsv \
  --p-where "[Source]='Mock'" \
  --o-filtered-table /data/mramseylab/Apr2020/MockQC/Mock-table.qza

qiime feature-table filter-features \
  --i-table /data/mramseylab/Apr2020/MockQC/Mock-table.qza \
  --m-metadata-file /data/mramseylab/classifiers/taxonomy.old.qza \
  --o-filtered-table /data/mramseylab/Apr2020/MockQC/Mock-table2.qza

#taxonomy.old.qza is the Silva one not the newer Greengenes attempt

qiime taxa barplot \
  --i-table /data/mramseylab/Apr2020/MockQC/Mock-table2.qza \
  --i-taxonomy /data/mramseylab/classifiers/taxonomy.old.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum3.tsv \
  --o-visualization /data/mramseylab/Apr2020/MockQC/Mock-bar-plots.qzv