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HybPhyloMaker9_update_trees.sh
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HybPhyloMaker9_update_trees.sh
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#!/bin/bash
#----------------MetaCentrum----------------
#PBS -l walltime=2:00:00
#PBS -l select=1:ncpus=1:mem=1gb:scratch_local=1gb
#PBS -j oe
#PBS -N HybPhyloMaker9_update_trees
#PBS -m abe
#-------------------HYDRA-------------------
#$ -S /bin/bash
#$ -q sThC.q
#$ -l mres=1G
#$ -cwd
#$ -j y
#$ -N HybPhyloMaker9_update_trees
#$ -o HybPhyloMaker9_update_trees.log
# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * https://github.com/tomas-fer/HybPhyloMaker *
# * Script 09 - Update trees *
# * v.1.8.0d *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2024 *
# * [email protected] *
# ********************************************************************************
#UPDATE on tree selection
#Requires 'gene_properties_update.txt' in
#$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/
#folder 'update' has to be manually created and 'gene_properties_update.txt' manually copied there
#'gene_properties_update.txt' is to be created from 'gene_properties.txt' by deleting lines with unwanted genes...
if [[ $PBS_O_HOST == *".cz" ]]; then
echo -e "\nHybPhyloMaker9 is running on MetaCentrum..."
#settings for MetaCentrum
#Move to scratch
cd $SCRATCHDIR
#Copy file with settings from home and set variables from settings.cfg
cp $PBS_O_WORKDIR/settings.cfg .
. settings.cfg
#. /packages/run/modules-2.0/init/bash
path=/storage/$server/home/$LOGNAME/$data
source=/storage/$server/home/$LOGNAME/HybSeqSource
#Add necessary modules
module add r/4.4.0-gcc-10.2.1-ssuwpvb
#module add debian11/compat #necessary for R-3.4.3
#module add R-3.4.3-gcc
#module add debian10-compat
#Set package library for R
export R_LIBS="/storage/$server/home/$LOGNAME/Rpackages44"
elif [[ $HOSTNAME == compute-*-*.local ]]; then
echo -e "\nHybPhyloMaker9 is running on Hydra..."
#settings for Hydra
#set variables from settings.cfg
. settings.cfg
path=../$data
source=../HybSeqSource
#Make and enter work directory
mkdir workdir09
cd workdir09
#Add necessary modules
module load tools/R/3.4.1
else
echo -e "\nHybPhyloMaker9 is running locally..."
#settings for local run
#set variables from settings.cfg
. settings.cfg
path=../$data
source=../HybSeqSource
#Make and enter work directory
mkdir workdir09
cd workdir09
fi
#Setting for the case when working with cpDNA
if [[ $cp =~ "yes" ]]; then
echo -en "Working with cpDNA"
type="cp"
else
echo -en "Working with exons"
type="exons"
fi
#Settings for selection and (un)corrected reading frame
if [ -z "$selection" ]; then
if [[ $corrected =~ "yes" ]]; then
mafftpath=$type/61mafft_corrected
alnpath=$type/80concatenated_exon_alignments_corrected
alnpathselected=$type/81selected_corrected
treepath=$type/82trees_corrected
echo -e "...with corrected reading frame\n"
else
mafftpath=$type/60mafft
alnpath=$type/70concatenated_exon_alignments
alnpathselected=$type/71selected
treepath=$type/72trees
echo -e "\n"
fi
else
if [[ $corrected =~ "yes" ]]; then
mafftpath=$type/$selection/61mafft_corrected
alnpath=$type/$selection/80concatenated_exon_alignments_corrected
alnpathselected=$type/$selection/81selected_corrected
treepath=$type/$selection/82trees_corrected
echo -e "...with corrected reading frame...and for selection: $selection\n"
else
mafftpath=$type/$selection/60mafft
alnpath=$type/$selection/70concatenated_exon_alignments
alnpathselected=$type/$selection/71selected
treepath=$type/$selection/72trees
echo -e "...and for selection: $selection\n"
fi
fi
#Test if updated gene selection exists
if [ ! -f "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/gene_properties_update.txt" ]; then
echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/gene_properties_update.txt' is missing. Exiting...\n"
rm -d ../workdir09 2>/dev/null
exit 3
fi
if [[ ! $location == "1" ]]; then
if [ "$(ls -A ../workdir09)" ]; then
echo -e "Directory 'workdir09' already exists and is not empty. Delete it or rename before running this script again. Exiting...\n"
rm -d ../workdir09 2>/dev/null
exit 3
fi
fi
#Write log
logname=HPM9
echo -e "HybPhyloMaker9: update trees" > ${logname}.log
if [[ $PBS_O_HOST == *".cz" ]]; then
echo -e "run on MetaCentrum: $PBS_O_HOST" >> ${logname}.log
elif [[ $HOSTNAME == compute-*-*.local ]]; then
echo -e "run on Hydra: $HOSTNAME" >> ${logname}.log
else
echo -e "local run: "`hostname`"/"`whoami` >> ${logname}.log
fi
echo -e "\nBegin:" `date '+%A %d-%m-%Y %X'` >> ${logname}.log
echo -e "\nSettings" >> ${logname}.log
if [[ $PBS_O_HOST == *".cz" ]]; then
printf "%-25s %s\n" `echo -e "\nServer:\t$server"` >> ${logname}.log
fi
for set in data selection cp corrected update MISSINGPERCENT SPECIESPRESENCE tree; do
printf "%-25s %s\n" `echo -e "${set}:\t" ${!set}` >> ${logname}.log
done
if [ ! -z "$selection" ]; then
echo -e "\nList of excluded samples" >> ${logname}.log
cat $source/excludelist.txt >> ${logname}.log
echo >> ${logname}.log
fi
#Copy scripts
cp $source/plotting_correlations.R .
cp $source/alignmentSummary.R .
cp $source/treepropsPlot.r .
#Set a log file for R outputs/error messages
touch R.log
#Copy updated gene list with properties (with unwanted genes deleted)
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/gene_properties_update.txt .
#Test if there is enough genes selected (i.e., 10 or more)
if [[ $(cat gene_properties_update.txt | wc -l) -lt 11 ]]; then
echo -e "Less than 10 genes selected. Exiting...\n"
cd ..
rm -r workdir09
exit 3
fi
#Plot gene properties correlations
cp gene_properties_update.txt combined.txt
echo -e "Plotting gene properties correlations for updated selection..."
echo -e "\nPlotting gene properties correlations for updated selection using plotting_correlations.R\n" >> R.log
if [ ! $location == "1" ]; then
#Run R script for correlation visualization (run via xvfb-run to enable generating PNG files without X11 server)
#echo "Running xvfb-run R..."
#xvfb-run R --slave -f plotting_correlations.R
R --slave -f plotting_correlations.R >> R.log 2>&1
else
R --slave -f plotting_correlations.R >> R.log 2>&1
fi
mv genes_corrs.png genes_corrs_update.png
mv genes_corrs.pdf genes_corrs_update.pdf
cp genes_corrs_update.* $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/
#Plot boxplots/histograms for selected alignment properties
cp gene_properties_update.txt summaryALL.txt
sed -i.bak 's/Aln_length/Alignment_length/' summaryALL.txt
sed -i.bak 's/Missing_perc/Missing_percent/' summaryALL.txt
sed -i.bak 's/Prop_pars_inf/Proportion_parsimony_informative/' summaryALL.txt
sed -i.bak 's/Aln_entropy/MstatX_entropy/' summaryALL.txt
echo -e "\nPlotting boxplots/histograms for alignment characteristics ..."
echo -e "\nPlotting boxplots/histograms for alignment characteristics using alignmentSummary.R ...\n" >> R.log
if [ ! $location == "1" ]; then
#Run R script for boxplot/histogram visualization (run via xvfb-run to enable generating PNG files without X11 server)
#xvfb-run R --slave -f alignmentSummary.R
R --slave -f alignmentSummary.R >> R.log 2>&1
else
R --slave -f alignmentSummary.R >> R.log 2>&1
fi
#Plot boxplots/histograms for selected tree properties
cp gene_properties_update.txt tree_stats_table.csv
cat tree_stats_table.csv | awk '{ print $34 "," $35 "," $36 "," $37 "," $38 "," $39 "," $40 "," $41 }' > tmp && mv tmp tree_stats_table.csv
sed -i.bak 's/Bootstrap/Average_bootstrap/' tree_stats_table.csv
sed -i.bak 's/Branch_length/Average_branch_length/' tree_stats_table.csv
sed -i.bak 's/P_distance/Avg_p_dist/' tree_stats_table.csv
sed -i.bak 's/Satur_slope/Slope/' tree_stats_table.csv
sed -i.bak 's/Satur_R_sq/R_squared/' tree_stats_table.csv
echo -e "\nPlotting boxplots/histograms for tree properties..."
echo -e "\nPlotting boxplots/histograms for tree properties using treepropsPlot.r\n" >> R.log
if [ ! $location == "1" ]; then
#Run R script for boxplot/histogram visualization (run via xvfb-run to enable generating PNG files without X11 server)
#xvfb-run R --slave -f treepropsPlot.r
R --slave -f treepropsPlot.r >> R.log 2>&1
else
R --slave -f treepropsPlot.r >> R.log 2>&1
fi
#Copy all resulting PNGs to home
cp *histogram.png $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/
#Copy R.log to home
cp R.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/
#Prepare list of genes of updated selection
cat gene_properties_update.txt | sed 1d | cut -f1 | sort | sed 's/Corrected//g' | sed "s/_modif${MISSINGPERCENT}.fas//g" > selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt
mkdir -p $path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes
cp selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt $path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes
echo -e "\nList of updated selected genes saved to $path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt..."
echo -e "Change 'update' to 'update=yes' in 'settings.cfg' and continue with running scripts 7 and 8..."
#Copy log to home
echo -e "\nEnd:" `date '+%A %d-%m-%Y %X'` >> ${logname}.log
cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/
#Clean scratch/work directory
if [[ $PBS_O_HOST == *".cz" ]]; then
#delete scratch
if [[ ! $SCRATCHDIR == "" ]]; then
rm -rf $SCRATCHDIR/*
fi
else
cd ..
rm -r workdir09
fi
echo -e "\nScript HybPhyloMaker9 finished...\n"