#!/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 taxa filter-table \
  --i-table /data/mramseylab/proc_reads/filtered/RunM-Human-Filter1-table.qza \
  --i-taxonomy /data/mramseylab/classifiers/taxonomy.qza \
  --p-mode contains \
  --p-exclude "Chloroplast" \
  --o-filtered-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza

qiime taxa filter-table \
  --i-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza \
  --i-taxonomy /data/mramseylab/classifiers/taxonomy.qza \
  --p-mode contains \
  --p-exclude "Mitochondria" \
  --o-filtered-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza

qiime taxa filter-table \
  --i-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza \
  --i-taxonomy /data/mramseylab/classifiers/taxonomy.qza \
  --p-mode contains \
  --p-exclude "Ralstonia" \
  --o-filtered-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza

qiime taxa filter-table \
  --i-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza \
  --i-taxonomy /data/mramseylab/classifiers/taxonomy.qza \
  --p-mode contains \
  --p-exclude "Chryseobacterium" \
  --o-filtered-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza

qiime taxa filter-table \
  --i-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza \
  --i-taxonomy /data/mramseylab/classifiers/taxonomy.qza \
  --p-mode contains \
  --p-exclude "Pseudomonas" \
  --o-filtered-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza

qiime taxa filter-table \
  --i-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza \
  --i-taxonomy /data/mramseylab/classifiers/taxonomy.qza \
  --p-mode contains \
  --p-exclude "Sphingomonas" \
  --o-filtered-table /data/mramseylab/proc_reads/filtered/RunM-Filter2-table.qza