#!/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

#note new $tablein below as we are now working on human only samples filtered in meta-filter.sh
tablein=/data/mramseylab/proc_reads/fil-nocontrol/table-filtered_NoControls.qza
clsdir=/data/mramseylab/classifiers/
metadir=/data/mramseylab/metadata/plaque_meta_2.tsv
visdir=/data/mramseylab/visualizations/

# filter status of input files, "minF-hum" is minimal filtered human only data
fil=MinFil_AL
filtdir=/data/mramseylab/proc_reads/

#must make the directory you are filtering to 1st or else it will error
mkdir $filtdir$fil

#filter features that appear less than 10 times across all samples
qiime feature-table filter-features \
  --i-table $tablein \
  --p-min-frequency 10 \
  --o-filtered-table $filtdir\MinFil-table_NC_AL.qza

#Making visualization at each step to monitor loss of taxa numbers
qiime feature-table summarize \
  --i-table $filtdir\MinFil-table_NC_AL.qza \
  --o-visualization $filtdir\MinFil-table_NC_AL.qzv \
  --m-sample-metadata-file $metadir \

#filter for features present in more than 2 libraries
qiime feature-table filter-features \
  --i-table $filtdir\MinFil-table_NC_AL.qza \
  --p-min-samples 3 \
  --o-filtered-table $filtdir\MinFil-table_NC_AL.qza

qiime feature-table summarize \
  --i-table $filtdir\MinFil-table_NC_AL.qza \
  --o-visualization $filtdir\MinFil-table_NC_AL_FEATSUM.qzv \
  --m-sample-metadata-file $metadir \

#Filter things with less than 20 reads per sample
qiime feature-table filter-samples \
  --i-table $filtdir\MinFil-table_NC_AL.qza \
  --p-min-frequency 20 \
  --o-filtered-table $filtdir\MinFil_20_AL.qza

qiime feature-table summarize \
  --i-table $filtdir\MinFil_20_AL.qza \
  --o-visualization $filtdir\MinFil_20_SUM_AL.qzv \
  --m-sample-metadata-file $metadir \

#View the *qzv tables and determine the sampling depth for the next steps (align-to-tree-mafft-fasttree)
#Use excluded table to generate barplot for checking