moving_picture_analysis.csh

#!/bin/sh
# 
#SBATCH --job-name=moving_pictures
#SBATCH --time=24:00:00
#SBATCH --partition=parallel
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --tasks-per-node=5
#SBATCH --mail-type=end 
#SBATCH --mail-user=jdodd7@jhu.edu


# load qiime module
module load qiime2/2023.5.1

# edit variables of config file according to analysis
# this script will use the variables in the config file for this analysis
# get proper classifier reminder - in config file
source ./moving_picture_analysis.config


# echo the time for each - this will help with debugging
echo "Starting moving picture tutorial analysis"
date

# sequence alignment and phylogenetic tree 
echo "Starting alignment and tree"
date

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences ${REPS} \
  --o-alignment ${PREFIX}_aligned-rep-seqs.qza \
  --o-masked-alignment ${PREFIX}_masked-aligned-rep-seqs.qza \
  --o-tree ${PREFIX}_unrooted-tree.qza \
  --o-rooted-tree ${PREFIX}_rooted-tree.qza

# alpha diversity:
echo "Starting alpha diversity"
date

qiime diversity core-metrics-phylogenetic \
  --i-phylogeny ${PREFIX}_rooted-tree.qza \
  --i-table ${TABLE} \
  --p-sampling-depth ${DEPTH} \
  --m-metadata-file ${METADATA} \
  --output-dir ${PREFIX}_core-metrics-results

# group significance
echo "Starting alpha diversity significance"
date

qiime diversity alpha-group-significance \
  --i-alpha-diversity ${PREFIX}_core-metrics-results/faith_pd_vector.qza \
  --m-metadata-file ${METADATA} \
  --o-visualization ${PREFIX}_core-metrics-results/faith-pd-group-significance.qzv

qiime diversity alpha-group-significance \
  --i-alpha-diversity ${PREFIX}_core-metrics-results/evenness_vector.qza \
  --m-metadata-file ${METADATA} \
  --o-visualization ${PREFIX}_core-metrics-results/evenness-group-significance.qzv

# beta diveristy
echo "Beta diversity"
date
qiime emperor plot \
  --i-pcoa ${PREFIX}_core-metrics-results/unweighted_unifrac_pcoa_results.qza \
  --m-metadata-file ${METADATA} \
  --o-visualization ${PREFIX}_core-metrics-results/unweighted-unifrac-emperor.qzv

qiime emperor plot \
  --i-pcoa ${PREFIX}_core-metrics-results/bray_curtis_pcoa_results.qza \
  --m-metadata-file ${METADATA} \
  --o-visualization ${PREFIX}_core-metrics-results/bray-curtis-emperor-days.qzv

# alpha rarefaction
echo "Alpha rarefaction"
date

qiime diversity alpha-rarefaction \
  --i-table ${TABLE} \
  --i-phylogeny ${PREFIX}_rooted-tree.qza \
  --p-max-depth ${DEPTH} \
  --m-metadata-file ${METADATA} \
  --o-visualization ${PREFIX}_alpha-rarefaction.qzv

# taxonomy
echo "Starting taxonomic analysis"
date

qiime feature-classifier classify-sklearn \
  --i-classifier ${CLASSI} \
  --i-reads ${REPS} \
  --o-classification ${PREFIX}_taxonomy.qza

qiime metadata tabulate \
  --m-input-file ${PREFIX}_taxonomy.qza \
  --o-visualization ${PREFIX}_taxonomy.qzv

qiime taxa barplot \
        --i-table ${TABLE} \
        --i-taxonomy ${PREFIX}_taxonomy.qza \
        --m-metadata-file ${METADATA} \
        --o-visualization ${PREFIX}_Lizzy_taxonomy_barplots.qzv

echo "End of script"
date