#!/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 feature-classifier extract-reads \
  --i-sequences /data/mramseylab/classifiers/silva_99_otus.qza \
  --p-f-primer AGAGTTTGATYMTGGCTCAG \
  --p-r-primer GWATTACCGCGGCKGCTG \
  --p-min-length 120 \
  --p-max-length 500 \
  --o-reads /data/mramseylab/classifiers/ref-seqs.qza


qiime feature-classifier fit-classifier-naive-bayes \
  --i-reference-reads /data/mramseylab/classifiers/ref-seqs.qza \
  --i-reference-taxonomy /data/mramseylab/classifiers/ref-taxonomy.qza \
  --o-classifier /data/mramseylab/classifiers/my_silva_classifier.qza