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q2pipe_step10_metrics.sh
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q2pipe_step10_metrics.sh
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#!/bin/bash
################################
# #
# Qiime 2 Pipeline #
# By: Patrick Gagne (NRCan) #
# Step 10 - Metrics Generation #
# Complete Version #
# september 8, 2023 #
# #
################################
exit_on_error(){
echo "Qiime2 command error detected"
echo "Exiting program"
exit 1
}
optionfile=$1
if [ ! $optionfile ] || [ ! -e $optionfile ] || [ ! -r $optionfile ]
then
echo "ERROR: you must specify a valid, accessible qiime2 optionfile"
exit 1
fi
source $optionfile
if [ $TEMPORARY_DIRECTORY ]
then
echo "Overriding default temporary directory to $TEMPORARY_DIRECTORY"
if [ ! -d $TEMPORARY_DIRECTORY ] || [ ! -w $TEMPORARY_DIRECTORY ]
then
echo "ERROR: $TEMPORARY_DIRECTORY does not exist or is read only"
exit 2
fi
export TMPDIR=$TEMPORARY_DIRECTORY
fi
if [ ! $TMPDIR ]
then
export TMPDIR=/tmp
fi
if [ "$APPTAINER_COMMAND" != "" ]
then
echo "DEBUG: Checking temporary folder"
temp_check=$( $APPTAINER_COMMAND mktemp -t Q2PIPE_TEMPFOLDER_CHECK.XXXXXX.temp )
bname=$( basename $temp_check )
if [ ! -e $TMPDIR/$bname ]
then
echo "ERROR: Disparity between Apptainer temporary folder and system temporary folder"
echo "Please make sure both are pointing to the same folder"
exit 5
else
echo "DEBUG: Temporary file check status: OK"
rm $TMPDIR/Q2PIPE_TEMPFOLDER_CHECK.??????.temp
fi
fi
detected_error=0
# Preparing list to be for-loop compatible
alpha_metrics=$( echo $alpha_metrics | sed 's/,/ /g' )
beta_metrics=$( echo $beta_metrics | sed 's/,/ /g' )
if [ "$SKIP_RAREFACTION" == "both" ]
then
SKIP_RAREFACTION="false true"
if [ -d $ANALYSIS_NAME.metrics_norarefaction_dn$p_perc_identity ] || [ -d $ANALYSIS_NAME.metrics_rarefied_"$p_sampling_depth"_dn"$p_perc_identity" ]
then
echo "ERROR: Previous metrics folder detected from previous run"
echo "Please delete the following folders if they exist:"
echo "$ANALYSIS_NAME.metrics_norarefaction_dn$p_perc_identity"
echo "$ANALYSIS_NAME.metrics_rarefied_"$p_sampling_depth"_dn"$p_perc_identity""
exit 3
fi
fi
for raref_param in $SKIP_RAREFACTION
do
if [ "$raref_param" == "true" ]
then
echo "Skip Rarefaction parameter detected"
echo "$ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza will be used"
input_table="$ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza"
output_f="$ANALYSIS_NAME.metrics_norarefaction_dn$p_perc_identity"
if [ -d $output_f ]
then
echo "ERROR: Folder $output_f already exist"
echo "Please delete this folder before proceeding"
exit 3
fi
mkdir $output_f
else
echo "Rarefaction parameter detected"
echo "$ANALYSIS_NAME.rarefied_"$p_sampling_depth"_filtered_table_dn"$p_perc_identity".qza will be used"
input_table="$ANALYSIS_NAME.rarefied_"$p_sampling_depth"_filtered_table_dn"$p_perc_identity".qza"
output_f="$ANALYSIS_NAME.metrics_rarefied_"$p_sampling_depth"_dn"$p_perc_identity""
if [ -d $output_f ]
then
echo "ERROR: Folder $output_f already exist"
echo "Please delete this folder before proceeding"
exit 3
fi
mkdir $output_f
mkdir $output_f/alpha_qza_export
mkdir $output_f/beta_qza_export
fi
#echo "Input table : $input_table"
for i in $alpha_metrics
do
(
echo "Calculating alpha diversity metric $i"
$APPTAINER_COMMAND qiime diversity alpha \
--i-table $input_table \
--p-metric $i \
--no-recycle \
--o-alpha-diversity $output_f/alpha_$i.qza || exit_on_error
$APPTAINER_COMMAND qiime diversity alpha-group-significance \
--i-alpha-diversity $output_f/alpha_$i.qza \
--m-metadata-file $METADATA_FILE_PATH \
--o-visualization $output_f/alpha_$i.qzv || detected_error=1
# NEW
$APPTAINER_COMMAND qiime tools export \
--input-path $output_f/alpha_$i.qza \
--output-path $output_f/alpha_qza_export/alpha_$i
) &
while [[ $(jobs -r -p | wc -l) -ge $NB_THREADS ]]; do
sleep 1
done
# not sure yet
#mv $output_f/alpha_qza_export/alpha_$i/alpha-diversity.tsv $output_f/alpha_qza_export/alpha_$i.tsv
#rm -rf $output_f/alpha_qza_export/alpha_$i
done
#wait
for i in $beta_metrics
do
(
echo "Calculating beta diversity metric $i"
$APPTAINER_COMMAND qiime diversity beta \
--i-table $input_table \
--p-metric $i \
--no-recycle \
--o-distance-matrix $output_f/beta_"$i"_distance_matrix.qza || exit_on_error
#--p-n-jobs $NB_THREADS \
$APPTAINER_COMMAND qiime diversity pcoa \
--i-distance-matrix $output_f/beta_"$i"_distance_matrix.qza \
--o-pcoa $output_f/beta_"$i"_pcoa.qza || exit_on_error
$APPTAINER_COMMAND qiime emperor plot \
--i-pcoa $output_f/beta_"$i"_pcoa.qza \
--m-metadata-file $METADATA_FILE_PATH \
--o-visualization $output_f/beta_"$i"_emperor.qzv || exit_on_error
# New
$APPTAINER_COMMAND qiime tools export \
--input-path $output_f/beta_"$i"_distance_matrix.qza \
--output-path $output_f/beta_qza_export/beta_"$i"_distance_matrix
$APPTAINER_COMMAND qiime tools export \
--input-path $output_f/beta_"$i"_pcoa.qza \
--output-path $output_f/beta_qza_export/beta_"$i"_pcoa
) &
while [[ $(jobs -r -p | wc -l) -ge $NB_THREADS ]]; do
sleep 1
done
# not sure yet
#mv $output_f/beta_qza_export/beta_"$i"_distance_matrix/distance-matrix.tsv $output_f/beta_qza_export/beta_"$i"_distance_matrix.tsv
#mv $output_f/beta_qza_export/beta_"$i"_pcoa/ordination.txt $output_f/beta_qza_export/beta_"$i"_pcoa_ordination.txt
#rm -rf $output_f/beta_qza_export/beta_"$i"_distance_matrix
#rm -rf $output_f/beta_qza_export/beta_"$i"_pcoa
done
#wait
if [ "$GENERATE_PHYLOGENY" == "true" ]
then
alpha_metrics_phylo=$( echo $alpha_metrics_phylo | sed 's/,/ /g' )
beta_metrics_phylo=$( echo $beta_metrics_phylo | sed 's/,/ /g' )
for i in $alpha_metrics_phylo
do
(
echo "Calculating phylogenetic alpha diversity metric $i"
$APPTAINER_COMMAND qiime diversity alpha-phylogenetic \
--i-table $input_table \
--i-phylogeny $ANALYSIS_NAME.rooted_tree.qza \
--p-metric $i \
--no-recycle \
--o-alpha-diversity $output_f/alpha_$i.phylo.qza || exit_on_error
$APPTAINER_COMMAND qiime diversity alpha-group-significance \
--i-alpha-diversity $output_f/alpha_$i.phylo.qza \
--m-metadata-file $METADATA_FILE_PATH \
--o-visualization $output_f/alpha_$i.phylo.qzv || detected_error=1
$APPTAINER_COMMAND qiime tools export \
--input-path $output_f/alpha_$i.phylo.qza \
--output-path $output_f/alpha_qza_export/alpha_"$i"_phylo
) &
while [[ $(jobs -r -p | wc -l) -ge $NB_THREADS ]]; do
sleep 1
done
done
#wait
for i in $beta_metrics_phylo
do
(
echo "Calculating phylogenetic beta diversity metric $i"
$APPTAINER_COMMAND qiime diversity beta-phylogenetic \
--i-table $input_table \
--i-phylogeny $ANALYSIS_NAME.rooted_tree.qza \
--p-metric $i \
--no-recycle \
--o-distance-matrix $output_f/beta_"$i"_distance_matrix.phylo.qza || exit_on_error
#--p-threads $NB_THREADS \
$APPTAINER_COMMAND qiime diversity pcoa \
--i-distance-matrix $output_f/beta_"$i"_distance_matrix.phylo.qza \
--o-pcoa $output_f/beta_"$i"_pcoa.phylo.qza || exit_on_error
$APPTAINER_COMMAND qiime emperor plot \
--i-pcoa $output_f/beta_"$i"_pcoa.phylo.qza \
--m-metadata-file $METADATA_FILE_PATH \
--o-visualization $output_f/beta_"$i"_emperor.phylo.qzv || exit_on_error
$APPTAINER_COMMAND qiime tools export \
--input-path $output_f/beta_"$i"_distance_matrix.phylo.qza \
--output-path $output_f/beta_qza_export/beta_"$i"_distance_matrix_phylo
$APPTAINER_COMMAND qiime tools export \
--input-path $output_f/beta_"$i"_pcoa.phylo.qza \
--output-path $output_f/beta_qza_export/beta_"$i"_pcoa_phylo
) &
while [[ $(jobs -r -p | wc -l) -ge $NB_THREADS ]]; do
sleep 1
done
done
#wait
fi
#wait
done
wait
if [ $detected_error -eq 1 ]
then
echo "WARNING: an alpha-group-significance step for one or more metrics returned an error"
fi
# Alpha Diversity $APPTAINER_COMMAND qiime diversity alpha \ --i-table
#$ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza \ --p-metric shannon \ --o-alpha-diversity
#$output_f/alpha_shannon.qza
#qiime diversity alpha-group-significance \
#--i-alpha-diversity $output_f/alpha_shannon.qza \
#--m-metadata-file $METADATA_FILE_PATH \
#--o-visualization $output_f/alpha_shannon.qzv
#$APPTAINER_COMMAND qiime tools export \
#--input-path $output_f/alpha_shannon.qza \
#--output-path $output_f/alpha_shannon.txt
#$APPTAINER_COMMAND qiime diversity alpha \
#--i-table $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza \
#--p-metric pielou_e \
#--o-alpha-diversity $output_f/alpha_pielou.qza
#$APPTAINER_COMMAND qiime tools export \
#--input-path $output_f/alpha_pielou.qza \
#--output-path $output_f/alpha_pielou.txt
#$APPTAINER_COMMAND qiime diversity alpha \
#--i-table $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza \
#--p-metric observed_features \
#--o-alpha-diversity $output_f/alpha_observedFeatures.qza
#$APPTAINER_COMMAND qiime tools export \
#--input-path $output_f/alpha_observedFeatures.qza \
#--output-path $output_f/alpha_observedFeatures.txt
# Beta Diversity
#$APPTAINER_COMMAND qiime diversity beta \
#--i-table $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza \
#--p-metric jaccard \
#--p-n-jobs $NB_THREADS \
#--o-distance-matrix $output_f/distance-matrix_jaccard.qza
#$APPTAINER_COMMAND qiime diversity pcoa \
#--i-distance-matrix $output_f/distance-matrix_jaccard.qza \
#--o-pcoa $output_f/pcoa_jaccard.qza
#$APPTAINER_COMMAND qiime emperor plot \
#--i-pcoa $output_f/pcoa_jaccard.qza \
#--m-metadata-file $METADATA_FILE_PATH \
#--o-visualization $output_f/pcoa_jaccard.qzv
#$APPTAINER_COMMAND qiime diversity core-metrics \
#--i-table $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza \
#--p-sampling-depth $p_sampling_depth \
#--m-metadata-file $METADATA_FILE_PATH \
#--output-dir $ANALYSIS_NAME.core-metrics-results-rarefied_"$p_sampling_depth"_dn"$p_perc_identity" --verbose || exit_on_error
#$APPTAINER_COMMAND qiime diversity alpha-group-significance \
#--i-alpha-diversity $ANALYSIS_NAME.core-metrics-results-rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/evenness_vector.qza \
#--m-metadata-file $METADATA_FILE_PATH \
#--o-visualization $ANALYSIS_NAME.core-metrics-results-rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/evenness-group-significance_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".qzv --verbose || exit_on_error
#$APPTAINER_COMMAND qiime diversity alpha-group-significance \
#--i-alpha-diversity $ANALYSIS_NAME.core-metrics-results-rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/shannon_vector.qza \
#--m-metadata-file $METADATA_FILE_PATH \
#--o-visualization $ANALYSIS_NAME.core-metrics-results-rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/shannon-group-significance_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".qzv --verbose || exit_on_error
#$APPTAINER_COMMAND qiime diversity alpha-group-significance \
#--i-alpha-diversity $ANALYSIS_NAME.core-metrics-results-rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/observed_features_vector.qza \
#--m-metadata-file $METADATA_FILE_PATH \
#--o-visualization $ANALYSIS_NAME.core-metrics-results-rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/observed_features-group-significance_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".qzv --verbose || exit_on_error
#$APPTAINER_COMMAND qiime diversity alpha \
#--i-table $ANALYSIS_NAME.rarefied_"$p_sampling_depth"_filtered_table_dn"$p_perc_identity".qza \
#--p-metric simpson \
#--o-alpha-diversity $ANALYSIS_NAME.core-metrics-results-rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/simpson_index_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".qza --verbose || exit_on_error
#$APPTAINER_COMMAND qiime diversity alpha-group-significance \
#--i-alpha-diversity $ANALYSIS_NAME.core-metrics-results-rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/simpson_index_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".qza \
#--m-metadata-file $METADATA_FILE_PATH \
#--o-visualization $ANALYSIS_NAME.core-metrics-results-rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/simpson_index-group-significance_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".qzv --verbose || exit_on_error