HybPhyloMaker8a2_astral4.sh

#!/bin/bash
#----------------MetaCentrum----------------
#PBS -l walltime=24:0:0
#PBS -l select=1:ncpus=4:mem=16gb:scratch_local=4gb
#PBS -j oe
#PBS -N HybPhyloMaker8a2_Astral4
#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 HybPhyloMaker8a2_Astral4
#$ -o HybPhyloMaker8a2_Astral4.log

# ********************************************************************************
# *    HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building    *
# *                  https://github.com/tomas-fer/HybPhyloMaker                  *
# *                     Script 08a2 - Astral-IV species tree                     *
# *                                   v.1.8.0                                    *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2024 *
# * tomas.fer@natur.cuni.cz                                                      *
# ********************************************************************************


#Compute species tree using ASTRAL-IV methods (with terminal and internal branch lengths in substitution-per-site units) from trees saved in a single gene tree file (with *.newick suffix)
#Run first
#(1) HybPhyloMaker5_missingdataremoval.sh with the same ${MISSINGPERCENT} and ${SPECIESPRESENCE} values
#(2) HybPhyloMaker6a_RAxML_for_selected.sh or HybPhyloMaker6b_FastTree_for_selected.sh with the same ${MISSINGPERCENT} and ${SPECIESPRESENCE} values
#(3) HybPhyloMaker7_roottrees.sh with the same ${MISSINGPERCENT} and ${SPECIESPRESENCE} values
#Works also for trees after update, requisite taxa selection and collapsing (see HybPhyloMaker9_update_trees.sh and HybPhyloMaker10_requisite_collapse.sh)
#Calculation of multilocus bootstrap is not implemented in ASTRAL-IV

#Complete path and set configuration for selected location
if [[ $PBS_O_HOST == *".cz" ]]; then
	echo -e "\nHybPhyloMaker8a2 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 jdk-1.6.0
	#Python (and its modules) are added later in the script
	#module add python-2.7.6-gcc
	#module add python27-modules-gcc
	#module add python-3.4.1-gcc
	module add newick-utils-13042016
	module add r/4.4.0-gcc-10.2.1-oxdi5pz
	#module add debian11/compat #necessary for R-3.4.3
	#module add R-3.4.3-gcc
	#module add debian8-compat
	#module add p4 #do not load before running 'python3 AMAS.py'
	#Set package library for R
	export R_LIBS="/storage/$server/home/$LOGNAME/Rpackages44"
	#available processors
	procavail=`expr $TORQUE_RESC_TOTAL_PROCS - 2`
elif [[ $HOSTNAME == compute-*-*.local ]]; then
	echo -e "\nHybPhyloMaker8a2 is running on Hydra..."
	#settings for Hydra
	#set variables from settings.cfg
	. settings.cfg
	path=../$data
	source=../HybSeqSource
	#Make and enter work directory
	mkdir -p workdir08a2
	cd workdir08a2
	#Add necessary modules
	module load java/1.7
	module load bioinformatics/anaconda3/5.1 #python3 and NewickUtilities
	module load tools/R/3.4.1
	#module load bioinformatics/newickutilities/0.0
	#module load bioinformatics/p4/ #???
else
	echo -e "\nHybPhyloMaker8a2 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 workdir08a2
	cd workdir08a2
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=$type/82trees_corrected
		echo -en "...with corrected reading frame"
	else
		mafftpath=$type/60mafft
		alnpath=$type/70concatenated_exon_alignments
		alnpathselected=$type/71selected
		treepath=$type/72trees
	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 -en "...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 -en "...and for selection: $selection"
	fi
fi

if [[ $update =~ "yes" ]]; then
	echo -e "...and with updated gene selection"
else
	echo -e ""
fi

if [[ ! $collapse -eq "0" ]]; then
	echo -e "...and with trees with branches below ${collapse} BS collapsed"
else
	if [[ $requisite =~ "no" ]]; then
		echo -e ""
	fi
fi

if [[ $requisite =~ "yes" ]]; then
	echo -e "...and only with trees with requisite taxa present\n"
else
	echo -e "\n"
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 necessary file
if [[ $requisite =~ "no" ]] && [[ $collapse -eq "0" ]];then
	echo -ne "Testing if input data are available..."
	if [[ $update =~ "yes" ]]; then
		if [ -z "$OUTGROUP" ]; then
			if [ -f "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_withoutBS.newick" ]; then
				if [[ $mlbs =~ "yes" ]]; then
					if [[ $tree =~ "RAxML" ]]; then
						if [ -f "$path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt" ]; then
							if [ 0 -lt $(ls $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/RAxML_bootstrap*ssembly_*_modif${MISSINGPERCENT}.result 2>/dev/null | wc -w) ]; then
								echo -e "OK\n"
							else
								echo -e "MLBS was requested but no bootstrap replicate trees were found in '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML'. Exiting..."
								rm -d ../workdir08a2 2>/dev/null
								exit 3
							fi
						else
							echo -e "'$path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt' is missing. Exiting...\n"
							rm -d ../workdir08a2 2>/dev/null
							exit 3
						fi
					elif [[ $tree =~ "FastTree" && $FastTreeBoot =~ "yes" ]]; then
						if [ -f "$path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt" ]; then
							if [ 0 -lt $(ls $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree/*ssembly_*_*.boot.fast.trees 2>/dev/null | wc -w) ]; then
								echo -e "OK\n"
							else
								echo -e "MLBS was requested but no bootstrap replicate trees were found in '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree'. Exiting..."
								rm -d ../workdir08a2 2>/dev/null
								exit 3
							fi
						else
							echo -e "'$path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt' is missing. Exiting...\n"
							rm -d ../workdir08a2 2>/dev/null
							exit 3
						fi
					fi
				else
					echo -e "OK\n"
				fi
			else
				echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_withoutBS.newick' is missing. Exiting...\n"
				rm -d ../workdir08a2 2>/dev/null
				exit 3
			fi
		else
			if [ -f "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick" ]; then
				if [[ $mlbs =~ "yes" ]]; then
					if [[ $tree =~ "RAxML" ]]; then
						if [ -f "$path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt" ]; then
							if [ 0 -lt $(ls $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/RAxML_bootstrap*ssembly_*_modif${MISSINGPERCENT}.result 2>/dev/null | wc -w) ]; then
								echo -e "OK\n"
							else
								echo -e "MLBS was requested but no bootstrap replicate trees were found in '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML'. Exiting..."
								rm -d ../workdir08a2 2>/dev/null
								exit 3
							fi
						else
							echo -e "'$path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt' is missing. Exiting...\n"
							rm -d ../workdir08a2 2>/dev/null
							exit 3
						fi
					elif [[ $tree =~ "FastTree" && $FastTreeBoot =~ "yes" ]]; then
						if [ -f "$path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt" ]; then
							if [ 0 -lt $(ls $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree/*ssembly_*_*.boot.fast.trees 2>/dev/null | wc -w) ]; then
								echo -e "OK\n"
							else
								echo -e "MLBS was requested but no bootstrap replicate trees were found in '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree'. Exiting..."
								rm -d ../workdir08a2 2>/dev/null
								exit 3
							fi
						else
							echo -e "'$path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt' is missing. Exiting...\n"
							rm -d ../workdir08a2 2>/dev/null
							exit 3
						fi
					fi
				else
					echo -e "OK\n"
				fi
			else
				echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick' is missing. Exiting...\n"
				rm -d ../workdir08a2 2>/dev/null
				exit 3
			fi
		fi
	else
		if [ -z "$OUTGROUP" ]; then
			if [ -f "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_withoutBS.newick" ]; then
				if [[ $mlbs =~ "yes" ]]; then
					if [[ $tree =~ "RAxML" ]]; then
						if [ 0 -lt $(ls $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/RAxML_bootstrap* 2>/dev/null | wc -w) ]; then
							echo -e "OK\n"
						else
							echo -e "MLBS was requested but no bootstrap replicate trees were found in '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML'. Exiting..."
							rm -d ../workdir08a2 2>/dev/null
							exit 3
						fi
					elif [[ $tree =~ "FastTree" && $FastTreeBoot =~ "yes" ]]; then
						if [ 0 -lt $(ls $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree/*.boot.fast.trees 2>/dev/null | wc -w) ]; then
							echo -e "OK\n"
						else
							echo -e "MLBS was requested but no bootstrap replicate trees were found in '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree'. Exiting..."
							rm -d ../workdir08a2 2>/dev/null
							exit 3
						fi
					fi
				else
					echo -e "OK\n"
				fi
			else
				echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_withoutBS.newick' is missing. Exiting...\n"
				rm -d ../workdir08a2 2>/dev/null
				exit 3
			fi
		else
			if [ -f "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick" ]; then
				if [[ $mlbs =~ "yes" ]]; then
					if [[ $tree =~ "RAxML" ]]; then
						if [ 0 -lt $(ls $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/RAxML_bootstrap* 2>/dev/null | wc -w) ]; then
							echo -e "OK\n"
						else
							echo -e "MLBS was requested but no bootstrap replicate trees were found in '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML'. Exiting..."
							rm -d ../workdir08a2 2>/dev/null
							exit 3
						fi
					elif [[ $tree =~ "FastTree" && $FastTreeBoot =~ "yes" ]]; then
						if [ 0 -lt $(ls $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree/*.boot.fast.trees 2>/dev/null | wc -w) ]; then
							echo -e "OK\n"
						else
							echo -e "MLBS was requested but no bootstrap replicate trees were found in '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree'. Exiting..."
							rm -d ../workdir08a2 2>/dev/null
							exit 3
						fi
					fi
				else
					echo -e "OK\n"
				fi
			else
				echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick' is missing. Exiting...\n"
				rm -d ../workdir08a2 2>/dev/null
				exit 3
			fi
		fi
	fi
	
	#Test if folder for results exits
	if [[ $update =~ "yes" ]]; then
		if [ -d "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/Astral4" ]; then
			echo -e "Directory '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/Astral4' already exists. Delete it or rename before running this script again. Exiting...\n"
			rm -d ../workdir08a2 2>/dev/null
			exit 3
		fi
	else
		if [ -d "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/Astral4" ]; then
			echo -e "Directory '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/Astral4' already exists. Delete it or rename before running this script again. Exiting...\n"
			rm -d ../workdir08a2 2>/dev/null
			exit 3
		fi
	fi
fi

if [[ ! $location == "1" ]]; then
	if [ "$(ls -A ../workdir08a)" ]; then
		echo -e "Directory 'workdir08a2' already exists and is not empty. Delete it or rename before running this script again. Exiting...\n"
		rm -d ../workdir08a2 2>/dev/null
		exit 3
	fi
fi

#Write log
logname=HPM8a2
echo -e "HybPhyloMaker8a2: ASTRAL-IV species tree" > ${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"` >> ${logname}.log
fi
for set in data selection cp corrected update MISSINGPERCENT SPECIESPRESENCE tree FastTreeBoot OUTGROUP collapse requisite mlbs combine astralt4; do
	printf "%-25s %s\n" `echo -e "${set}:\t" ${!set}` >> ${logname}.log
done
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

#Copy genetree file
if [[ $update =~ "yes" ]]; then
	if [ -z "$OUTGROUP" ]; then
		cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}${treefile} .
		#mv trees${MISSINGPERCENT}_${SPECIESPRESENCE}_withoutBS.newick trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick
		mv $treefile trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick
	else
		cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}${treefile} .
		mv $treefile trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick
	fi
else
	if [ -z "$OUTGROUP" ]; then
		cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}${treefile} .
		#mv trees${MISSINGPERCENT}_${SPECIESPRESENCE}_withoutBS.newick trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick
		mv $treefile trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick
	else
		cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}${treefile} .
		mv $treefile trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick
	fi
fi

#Modify labels in gene tree
sed -i.bak 's/XX/-/g' trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick
sed -i.bak2 's/YY/_/g' trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick

#Check if OUTGROUP does exist in gene tree files
if [ ! -z "$OUTGROUP" ]; then #only if outgroup is set
	if [ -z $(grep $OUTGROUP trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick) ]; then
		echo -e "$OUTGROUP was not found in gene tree file. Exiting..."
		exit 3
	fi
fi
if [[ $collapse -eq "0" ]];then
	if [[ $mlbs =~ "yes" ]]; then
		#Copy bootrapped gene tree files (if tree=RAxML or tree=FastTree and FastTreeBoot=yes)
		if [[ $tree =~ "RAxML" ]]; then
			#Make dir for for bootstraped trees
			mkdir boot
			#Copy RAxML bootstraped trees
			if [[ $update =~ "yes" ]]; then
				if [[ $requisite =~ "yes" ]]; then
					cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite/selected_genes_with_requisite.txt .
					mv selected_genes_with_requisite.txt selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt
				else
					cp $path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt .
				fi
				for i in $(cat selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt); do
					cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/RAxML_bootstrap*ssembly_${i}_modif${MISSINGPERCENT}.result boot/
				done
			else
				if [[ $requisite =~ "yes" ]]; then
					cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite/selected_genes_with_requisite.txt .
					for i in $(cat selected_genes_with_requisite.txt); do
						cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/RAxML_bootstrap*ssembly_${i}_modif${MISSINGPERCENT}.result boot/
					done
				else
					cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/RAxML/RAxML_bootstrap* boot/
				fi
			fi
			#Make a list of bootstrapped trees
			ls boot/*bootstrap* > bs-files
		elif [[ $tree =~ "FastTree" && $FastTreeBoot =~ "yes" ]]; then
			#Make dir for for bootstrapped trees
			mkdir boot
			#Copy FastTree bootstrapped trees
			if [[ $update =~ "yes" ]]; then
				if [[ $requisite =~ "yes" ]]; then
					cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/with_requisite/selected_genes_with_requisite.txt .
					mv selected_genes_with_requisite.txt selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt
				else
					cp $path/${alnpathselected}${MISSINGPERCENT}/updatedSelectedGenes/selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt .
				fi
				for i in $(cat selected_genes_${MISSINGPERCENT}_${SPECIESPRESENCE}_update.txt); do
					cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree/*ssembly_${i}_*.boot.fast.trees boot/
				done
			else
				if [[ $requisite =~ "yes" ]]; then
					cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/with_requisite/selected_genes_with_requisite.txt .
					for i in $(cat selected_genes_with_requisite.txt); do
						cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree/*ssembly_${i}_*.boot.fast.trees boot/
					done
				else
					cp $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/FastTree/*.boot.fast.trees boot/
				fi
			fi
			#Make a list of bootstrapped trees
			ls boot/*.boot.fast.trees > bs-files
		fi
	fi
fi

if [[ $cp =~ "yes" ]]; then
	#Removing '_cpDNA' from gene trees in trees.newick
	if [ -d "boot" ]; then
		sed -i.bak 's/_cpDNA//g' boot/*
	fi
fi

#Make dir for results
if [[ $update =~ "yes" ]]; then
	mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral4
else
	mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral4
fi

#Run ASTRAL
#download Astral-IV
wget https://github.com/chaoszhang/ASTER/raw/refs/heads/Linux/bin/astral4
chmod +x astral4
if [ ! -z "$OUTGROUP" ]; then
	echo -e "Computing rooted ASTRAL-IV tree..."
	./astral4 --root ${OUTGROUP} -t ${procavail} -i trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick -o Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre 2> Astral.log
else
	echo -en "Computing unrooted ASTRAL-IV tree..."
	./astral4 -t ${procavail} -i trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick -o Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre 2> Astral.log
	echo -e "and post-ASTRAL re-rooting"
	nw_reroot -s Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre $OUTGROUP > tmp && mv tmp Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre
fi

#Make a copy of the main Astral tree for future combination(s)
cp Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}main.tre
sed -i.bak 's/-/XX/g' Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}main.tre
sed -i.bak2 's/_/YY/g' Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}main.tre

#Modify labels in Astral trees
sed -i.bak 's/-/ /g' Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre
sed -i.bak2 's/_/ /g' Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre

#Rename Astral trees
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

#Copy species tree and log to home
if [[ $update =~ "yes" ]]; then
	cp Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral/${astraltree}
	cp Astral*.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}Astral
else
	cp Astral_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral/${astraltree}
	cp Astral*.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral
fi

echo -e "Progress of ASTRAL run is written to Astral.log..."

#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
else
	cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}Astral
fi

#Clean scratch/work directory
if [[ $PBS_O_HOST == *".cz" ]]; then
	#delete scratch
	if [[ ! $SCRATCHDIR == "" ]]; then
		rm -rf $SCRATCHDIR/*
	fi
else
	cd ..
	rm -r workdir08a2
fi

echo -e "\nScript HybPhyloMaker8a2 finished...\n"