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HybPhyloMaker11_phyparts.sh
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#!/bin/bash
#----------------MetaCentrum----------------
#PBS -l walltime=24:0:0
#PBS -l select=1:ncpus=2:mem=16gb:scratch_local=4gb
#PBS -j oe
#PBS -N HybPhyloMaker11_PhyParts_Astral
#PBS -m abe
#-------------------HYDRA-------------------
#$ -S /bin/bash
#$ -pe mthread 4
#$ -q sThM.q
#$ -l mres=4G,h_data=4G,h_vmem=4G,himem
#$ -cwd
#$ -j y
#$ -N HybPhyloMaker11_PhyParts_Astral
#$ -o HybPhyloMaker11_PhyParts_Astral.log
# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * https://github.com/tomas-fer/HybPhyloMaker *
# * Script 11 - PhyParts for Astral species tree *
# * v.1.8.0d *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2025 *
# * tomas.fer@natur.cuni.cz *
# ********************************************************************************
#Runs PhyParts and PhyParts PieCharts for ASTRAL tree
#Takes all selected gene trees and only select trees with outgroup
#requires run on MetaCentrum or installation with 'install_software.sh'
#(i.e., 'phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar' must be in HybSeqSource (or in /usr/local/bin/)
#Complete path and set configuration for selected location
if [[ $PBS_O_HOST == *".cz" ]]; then
echo -e "\nHybPhyloMaker11_PhyParts 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 phyparts-0.0.1
module add newick-utils-13042016
elif [[ $HOSTNAME == compute-*-*.local ]]; then
echo -e "\nHybPhyloMaker11_PhyParts is running on Hydra..."
#settings for Hydra
#set variables from settings.cfg
. settings.cfg
path=../$data
source=../HybSeqSource
#Make and enter work directory
mkdir -p workdir11
cd workdir11
#Add necessary modules
module load bioinformatics/anaconda3/5.1 #adds NewickUtilities
module load ???phyparts#???
echo "PhyParts not yet installed on Hydra, exiting..."
exit 3
else
echo -e "\nHybPhyloMaker11_PhyParts is running locally..."
#settings for local run
#set variables from settings.cfg
. settings.cfg
path=../$data
source=../HybSeqSource
#Make and enter work directory
mkdir -p workdir11
cd workdir11
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=$type/82trees_corrected
echo -e "...with corrected reading frame"
else
mafftpath=$type/60mafft
alnpath=$type/70concatenated_exon_alignments
alnpathselected=$type/71selected
treepath=$type/72trees
echo -e ""
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: $selection"
else
mafftpath=$type/$selection/60mafft
alnpath=$type/$selection/70concatenated_exon_alignments
alnpathselected=$type/$selection/71selected
treepath=$type/$selection/72trees
echo -e "...and for selection: $selection"
fi
fi
if [[ $update =~ "yes" ]]; then
echo -e "...and with updated gene selection"
fi
if [[ ! $collapse -eq "0" ]]; then
echo -e "...and with trees with branches below ${collapse} BS collapsed"
else
if [[ $requisite =~ "no" ]]; then
echo -e "\n"
fi
fi
if [[ $requisite =~ "yes" ]]; then
echo -e "...and only with trees with requisite taxa present\n"
fi
if [[ ! $location == "1" ]]; then
if [ "$(ls -A ../workdir11)" ]; then
echo -e "Directory 'workdir11' already exists and is not empty. Delete it or rename before running this script again. Exiting...\n"
rm -d ../workdir11 2>/dev/null
exit 3
fi
fi
#Write log
logname=HPM11
echo -e "HybPhyloMaker11: PhyParts for Astral species tree" > ${logname}.log
if [[ $PBS_O_HOST == *".cz" ]]; then
echo -e "Job run on MetaCentrum: $PBS_JOBID" >> ${logname}.log
echo -e "From: $PBS_O_HOST" >> ${logname}.log
echo -e "Host: $HOSTNAME" >> ${logname}.log
echo -e "$PBS_NUM_NODES node(s) with $PBS_NCPUS core(s)" >> ${logname}.log
memM=$(bc <<< "scale=2; $(echo $PBS_RESC_MEM) / 1024 / 1024 ")
memG=$(bc <<< "scale=2; $(echo $PBS_RESC_MEM) / 1024 / 1024 / 1024 ")
if (( $(echo $memG 1 | awk '{if ($1 < $2) print 1;}') )); then
echo -e "Memory: $memM Mb" >> ${logname}.log
else
echo -e "Memory: $memG Gb" >> ${logname}.log
fi
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"` >> ${logname}.log
fi
ppcolors=${ppcolors// /-} #change ' ' in ${ppcolors} to '-'
for set in data selection cp corrected update MISSINGPERCENT SPECIESPRESENCE tree OUTGROUP collapse requisite phypartsbs ppcolors nrpptrees; do
printf "%-25s %s\n" `echo -e "${set}:\t" ${!set}` >> ${logname}.log
done
ppcolors=${ppcolors//-/ } #change '-' in ${ppcolors} back to ' '
if [[ $requisite =~ "yes" ]]; then
echo -e "\nList of requisite samples" >> ${logname}.log
echo $requisitetaxa | tr '|' '\n' >> ${logname}.log
fi
if [ ! -z "$selection" ]; then
echo -e "\nList of excluded samples" >> ${logname}.log
cat $source/excludelist.txt >> ${logname}.log
echo >> ${logname}.log
fi
#Settings for collapsed and requisite selection
if [[ $requisite =~ "yes" ]]; then
if [[ ! $collapse -eq "0" ]]; then
modif=with_requisite/collapsed${collapse}/
treefile=trees_with_requisite_collapsed${collapse}.newick
else
modif=with_requisite/
if [ -z "$OUTGROUP" ]; then
treefile=trees_with_requisite.newick
else
treefile=trees_rooted_with_requisite.newick
fi
fi
else
if [[ ! $collapse -eq "0" ]]; then
modif=collapsed${collapse}/
treefile=trees_collapsed${collapse}.newick
else
modif=""
if [ -z "$OUTGROUP" ]; then
treefile=trees.newick
else
treefile=trees_rooted.newick
fi
fi
fi
#Check if $OUTGROUP is set
if [ -z $OUTGROUP ]; then
echo -e "Outgroup is not set. Exiting..."
rm -d ../workdir11 2>/dev/null
exit 3
fi
#Define Astral tree name
if [[ $requisite =~ "yes" ]]; then
if [[ ! $collapse -eq "0" ]]; then
astraltree=Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}_with_requisite_collapsed${collapse}.tre
else
astraltree=Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}_with_requisite.tre
fi
else
if [[ ! $collapse -eq "0" ]]; then
astraltree=Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}_collapsed${collapse}.tre
else
astraltree=Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre
fi
fi
#Remove '.tre' from species tree name
sptree=$(cut -d'.' -f1 <<< $astraltree)
#Copy species tree
echo -e "\nCopying trees..."
if [[ $update =~ "yes" ]]; then
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/${astraltree} .
else
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/${astraltree} .
fi
#Copy gene trees (file with all gene trees)
if [[ $update =~ "yes" ]]; then
if [ -z "$OUTGROUP" ]; then
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}${treefile} .
else
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}${treefile} .
fi
else
if [ -z "$OUTGROUP" ]; then
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}${treefile} .
else
cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}${treefile} .
fi
fi
#Modify Astral tree (replace ' ' back to '-' and '_')
sed -i 's/ \([^ ]*\) / \1_/g' ${sptree}.tre #replace every second occurrence of ' ' by '_'
sed -i 's/ /-/g' ${sptree}.tre #replace all spaces by '-'
#Reroot Astral tree with $OUTGROUP
nw_reroot -s ${sptree}.tre $OUTGROUP > tmp && mv tmp ${sptree}.tre
#Modify labels in gene tree
sed -i.bak 's/XX/-/g' $treefile
sed -i.bak2 's/YY/_/g' $treefile
#Get only rooted gene trees (i.e., trees containing outgroup)
nrgenetreesorig=$(wc -l < $treefile)
grep "$OUTGROUP" ${treefile} > tmp
mv tmp ${treefile}
#Check if there are any gene trees left
if [ $(wc -l < ${treefile}) -eq 0 ]; then
echo -e "\nThere are no gene trees rooted with ${OUTGROUP}. Exiting..."
exit 3
fi
#Reroot genestrees with $OUTGROUP
nw_reroot -s ${treefile} $OUTGROUP > tmp && mv tmp ${treefile}
#Put single tree per file to directory 'trees'
mkdir trees
split -a 4 -d -l 1 ${treefile} trees/tree_
nrgenetreesrooted=$(ls trees/tree_* | wc -l)
#Subselect only first 'nrpptrees' if necessary (to decrease running time)
if [ -z "$nrpptrees" ]; then #test whether $nrpptrees is empty
nrpptrees=$nrgenetreesrooted #if empty set to number of rooted gene trees
fi
if [ $nrpptrees -gt $nrgenetreesrooted ]; then #test whether $nrpptrees is higher than nr. of rooted trees
nrpptrees=$nrgenetreesrooted #if higher set to number of rooted gene trees
fi
if [ $nrpptrees -lt $nrgenetreesrooted ]; then
echo -e "\nSubselecting $nrpptrees trees..."
mkdir trees$nrpptrees
cd trees
ls tree_* | head -n $nrpptrees | xargs -I{} cp "{}" ../trees$nrpptrees/
cd ..
rm -r trees
mv trees$nrpptrees trees
fi
#Calculate number of gene trees
nrgenetrees=$(ls trees/tree_* | wc -l)
#Set to 0.5 if $phypartsbs is empty
if [ -z "$phypartsbs" ]; then #test whether $phypartsbs is empty
echo -e "\n'phypartsbs' is not set to any value, using 0.5..."
phypartsbs=0.5
fi
#Statisctics
echo -e "\nSpecies tree: ${sptree}.tre" | tee -a phypartsinfo_BS${phypartsbs}_${nrpptrees}trees.txt
echo -e "Gene tree file: ${treefile}" | tee -a phypartsinfo_BS${phypartsbs}_${nrpptrees}trees.txt
echo -e "Nr. gene trees: ${nrgenetreesorig}" | tee -a phypartsinfo_BS${phypartsbs}_${nrpptrees}trees.txt
echo -e "Nr. gene trees rooted with '$OUTGROUP': ${nrgenetreesrooted}" | tee -a phypartsinfo_BS${phypartsbs}_${nrpptrees}trees.txt
echo -e "Using $nrpptrees gene trees" | tee -a phypartsinfo_BS${phypartsbs}_${nrpptrees}trees.txt
#Make dir for results
if [[ $update =~ "yes" ]]; then
mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/phyparts_${phypartsbs}
mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/phyparts_${phypartsbs}/trees_res_${nrpptrees}trees
else
mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/phyparts_${phypartsbs}
mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/phyparts_${phypartsbs}/trees_res_${nrpptrees}trees
fi
#Run phyparts
echo -e "\nRunning PhyParts with support cutoff ${phypartsbs}..."
# -a what kind of analysis (0 - concon, 1 - fullconcon, 2 - duplications)
# -d directory of trees
# -m mapping tree (species tree)
# -o prepend output files with this
# -s support cutoff (only keep things with greater support than the one specified)
# -v include verbose output
if [[ $location =~ "0" ]]; then
#download java PhyParts
cp /usr/local/bin/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar .
cp $source/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar .
echo "java -jar phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar -a 1 -d trees -m ${sptree}.tre -o trees_res -s ${phypartsbs} -v"
java -jar phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar -a 1 -d trees -m ${sptree}.tre -o trees_res -s ${phypartsbs} -v > phyparts.log 2>&1
else
echo "phyparts -a 1 -d trees -m ${sptree}.tre -o trees_res -s ${phypartsbs} -v"
phyparts -a 1 -d trees -m ${sptree}.tre -o trees_res -s ${phypartsbs} -v > phyparts.log 2>&1
#java -jar /software/phyparts/0.0.1/target/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar -a 1 -d trees -m ${sptree}.tre -o trees_res -s ${phypartsbs} -v > phyparts.log 2>&1
fi
#Run phypartspiecharts
echo -e "\nRunning PhyParts PieCharts..."
echo -e "Using colours: ${ppcolors}"
# --svg_name name of the resulting graphics
# species tree
# prefix of phypart results (i.e., the same as '-o' option in phyparts)
# number of genetrees
if [[ $location =~ "0" ]]; then
#download python script
wget https://raw.githubusercontent.com/mossmatters/phyloscripts/master/phypartspiecharts/phypartspiecharts.py 2>/dev/null
export QT_QPA_PLATFORM='offscreen' #for machines with commandline only
export XDG_RUNTIME_DIR=$(echo `pwd`) #current dir
if [ -z "$ppcolors" ]; then
echo "python3 phypartspiecharts.py --svg_name phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg ${sptree}.tre trees_res ${nrgenetrees}"
python3 phypartspiecharts.py --svg_name phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg ${sptree}.tre trees_res ${nrgenetrees} 2>/dev/null
else
echo "python3 phypartspiecharts.py --svg_name phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg ${sptree}.tre trees_res ${nrgenetrees} --colors ${ppcolors}"
python3 phypartspiecharts.py --svg_name phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg ${sptree}.tre trees_res ${nrgenetrees} --colors ${ppcolors} 2>/dev/null
#python /software/phyparts/0.0.1/target/phypartspiecharts.py --svg_name phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg ${sptree}.tre trees_res ${nrgenetrees} --colors ${ppcolors}
fi
else
if [ -z "$ppcolors" ]; then
echo "phypartspiecharts --svg_name phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg ${sptree}.tre trees_res ${nrgenetrees}"
phypartspiecharts --svg_name phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg ${sptree}.tre trees_res ${nrgenetrees}
else
echo "phypartspiecharts --svg_name phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg ${sptree}.tre trees_res ${nrgenetrees} --colors ${ppcolors}"
phypartspiecharts --svg_name phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg ${sptree}.tre trees_res ${nrgenetrees} --colors ${ppcolors}
#python /software/phyparts/0.0.1/target/phypartspiecharts.py --svg_name phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg ${sptree}.tre trees_res ${nrgenetrees} --colors ${ppcolors}
fi
fi
#Convert SVG to PDF
if [[ $PBS_O_HOST == *".cz" ]]; then
module add python36-modules-gcc #adds also cairosvg
fi
cairosvg phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg -o phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.pdf
#Copy results to home
if [[ $update =~ "yes" ]]; then
cp phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/phyparts_${phypartsbs}
cp phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.pdf $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/phyparts_${phypartsbs}
cp phypartsinfo_BS${phypartsbs}_${nrpptrees}trees.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/phyparts_${phypartsbs}
cp trees_res.*node* $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/phyparts_${phypartsbs}/trees_res_${nrpptrees}trees
cp trees_res.*hist* $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/phyparts_${phypartsbs}/trees_res_${nrpptrees}trees
cp phyparts.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/phyparts_${phypartsbs}/trees_res_${nrpptrees}trees
else
cp phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.svg $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/phyparts_${phypartsbs}
cp phyparts_${sptree}_BS${phypartsbs}_${nrpptrees}trees.pdf $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/phyparts_${phypartsbs}
cp phypartsinfo_BS${phypartsbs}_${nrpptrees}trees.txt $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/phyparts_${phypartsbs}
cp trees_res.*node* $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/phyparts_${phypartsbs}/trees_res_${nrpptrees}trees
cp trees_res.*hist* $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/phyparts_${phypartsbs}/trees_res_${nrpptrees}trees
cp phyparts.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/phyparts_${phypartsbs}/trees_res_${nrpptrees}trees
fi
#Copy log to home
echo -e "\nEnd:" `date '+%A %d-%m-%Y %X'` >> ${logname}.log
if [[ $update =~ "yes" ]]; then
cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/phyparts_${phypartsbs}
else
cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/phyparts_${phypartsbs}
fi
#Clean scratch/work directory
if [[ $PBS_O_HOST == *".cz" ]]; then
#delete scratch
if [[ ! $SCRATCHDIR == "" ]]; then
rm -rf $SCRATCHDIR/*
fi
else
cd ..
rm -r workdir11
fi
echo -e "\nScript HybPhyloMaker11 finished...\n"