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HybPhyloMaker8c_mrl.sh
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HybPhyloMaker8c_mrl.sh
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#!/bin/bash
#----------------MetaCentrum----------------
#PBS -l walltime=12:0:0
#PBS -l select=1:ncpus=8:mem=4gb:scratch_local=8gb
#PBS -j oe
#PBS -N HybPhyloMaker8c_MRL
#PBS -m abe
#-------------------HYDRA-------------------
#$ -S /bin/bash
#$ -pe mthread 8
#$ -q sThC.q
#$ -l mres=4G,h_data=4G,h_vmem=4G
#$ -cwd
#$ -j y
#$ -N HybPhyloMaker8c_MRL
#$ -o HybPhyloMaker8c_MRL.log
# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * https://github.com/tomas-fer/HybPhyloMaker *
# * Script 08c - MRL species tree *
# * v.1.8.0a *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2021 *
# * tomas.fer@natur.cuni.cz *
# ********************************************************************************
#Compute species tree using MRL methods using RAxML from trees saved in single gene tree file (with *.newick suffix)
#RAxML options: standard/rapid bootstrap (raxmlboot=), number of bootstrap replicates (bsrep=)
#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)
#Complete path and set configuration for selected location
if [[ $PBS_O_HOST == *".cz" ]]; then
echo -e "\nHybPhyloMaker8c 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
module add raxml-8.2.4
module add newick-utils-13042016
elif [[ $HOSTNAME == compute-*-*.local ]]; then
echo -e "\nHybPhyloMaker8c is running on Hydra..."
#settings for Hydra
#set variables from settings.cfg
. settings.cfg
path=../$data
source=../HybSeqSource
#Make and enter work directory
mkdir -p workdir08c
cd workdir08c
#Add necessary modules
module load java/1.7
module load bioinformatics/raxml/8.2.11
module load bioinformatics/anaconda3/5.1 #NewickUtilities
else
echo -e "\nHybPhyloMaker8c 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 workdir08c
cd workdir08c
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}_${SPECIESPRESENCE}_withoutBS.newick" ]; then
echo -e "OK\n"
else
echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_withoutBS.newick' is missing. Exiting...\n"
rm -d ../workdir08c 2>/dev/null
exit 3
fi
else
if [ -f "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick" ]; then
echo -e "OK\n"
else
echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick' is missing. Exiting...\n"
rm -d ../workdir08c 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
echo -e "OK\n"
else
echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_withoutBS.newick' is missing. Exiting...\n"
rm -d ../workdir08c 2>/dev/null
exit 3
fi
else
if [ -f "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick" ]; then
echo -e "OK\n"
else
echo -e "'$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick' is missing. Exiting...\n"
rm -d ../workdir08c 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/MRL" ]; then
echo -e "Directory '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/MRL' already exists. Delete it or rename before running this script again. Exiting...\n"
rm -d ../workdir08c 2>/dev/null
exit 3
fi
else
if [ -d "$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/MRL" ]; then
echo -e "Directory '$path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/MRL' already exists. Delete it or rename before running this script again. Exiting...\n"
rm -d ../workdir08c 2>/dev/null
exit 3
fi
fi
fi
if [[ ! $location == "1" ]]; then
if [ "$(ls -A ../workdir08c)" ]; then
echo -e "Directory 'workdir08c' already exists and is not empty. Delete it or rename before running this script again. Exiting...\n"
rm -d ../workdir08c 2>/dev/null
exit 3
fi
fi
#Write log
logname=HPM8c
echo -e "HybPhyloMaker8c: MRL 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"` >> ${logname}.log
fi
for set in data selection cp corrected update MISSINGPERCENT SPECIESPRESENCE tree OUTGROUP collapse requisite raxmlboot bsrep; do
printf "%-25s %s\n" `echo -e "${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
#Add necessary programs and files
cp $source/mrp.jar .
#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
#Make dir for results
if [[ $update =~ "yes" ]]; then
mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}MRL
else
mkdir $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}MRL
fi
#Make MRP matrix
echo -e "Preparing MRL matrix...\n"
#java -jar mrp.jar trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick MRPmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.nex NEXUS
#Make MRL matrix
if [[ $location == "2" ]]; then
java -d64 -server -XX:MaxHeapSize=4g -jar mrp.jar trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip PHYLIP -randomize
else
java -jar mrp.jar trees${MISSINGPERCENT}_${SPECIESPRESENCE}_rooted_withoutBS.newick MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip PHYLIP -randomize
fi
#Make bootstrap ML trees using RAxML
if [[ $raxmlboot == "standard" ]]; then
echo -e "Computing $bsrep standard bootstrap replicates using RAxML...\n"
if [[ $location == "1" ]]; then
raxmlHPC-PTHREADS -T $TORQUE_RESC_TOTAL_PROCS -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n bestML -m BINCAT -p 12345
raxmlHPC-PTHREADS -T $TORQUE_RESC_TOTAL_PROCS -b 12345 -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n boot -m BINCAT -p 12345 -N $bsrep
raxmlHPC-PTHREADS -T $TORQUE_RESC_TOTAL_PROCS -f b -t RAxML_bestTree.bestML -z RAxML_bootstrap.boot -n MRLresult -m BINCAT -p 12345
mv RAxML_bootstrap.boot RAxML_bootstrap.MRLresult
mv RAxML_bestTree.bestML RAxML_bestTree.MRLresult
cat RAxML_info.bestML RAxML_info.boot RAxML_info.MRLresult > tmp && mv tmp RAxML_info.MRLresult
elif [[ $location == "2" ]]; then
raxmlHPC-PTHREADS-SSE3 -T $NSLOTS -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n bestML -m BINCAT -p 12345
raxmlHPC-PTHREADS-SSE3 -T $NSLOTS -b 12345 -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n boot -m BINCAT -p 12345 -N $bsrep
raxmlHPC-PTHREADS-SSE3 -T $NSLOTS -f b -t RAxML_bestTree.bestML -z RAxML_bootstrap.boot -n MRLresult -m BINCAT -p 12345
mv RAxML_bootstrap.boot RAxML_bootstrap.MRLresult
mv RAxML_bestTree.bestML RAxML_bestTree.MRLresult
cat RAxML_info.bestML RAxML_info.boot RAxML_info.MRLresult > tmp && mv tmp RAxML_info.MRLresult
elif [[ $numbcores == "1" ]]; then
$raxmlseq -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n bestML -m BINCAT -p 12345
$raxmlseq -b 12345 -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n boot -m BINCAT -p 12345 -N $bsrep
$raxmlseq -f b -t RAxML_bestTree.bestML -z RAxML_bootstrap.boot -n MRLresult -m BINCAT -p 12345
mv RAxML_bootstrap.boot RAxML_bootstrap.MRLresult
mv RAxML_bestTree.bestML RAxML_bestTree.MRLresult
cat RAxML_info.bestML RAxML_info.boot RAxML_info.MRLresult > tmp && mv tmp RAxML_info.MRLresult
else
$raxmlpthreads -T $numbcores -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n bestML -m BINCAT -p 12345
$raxmlpthreads -T $numbcores -b 12345 -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n boot -m BINCAT -p 12345 -N $bsrep
$raxmlpthreads -T $numbcores -f b -t RAxML_bestTree.bestML -z RAxML_bootstrap.boot -n MRLresult -m BINCAT -p 12345
mv RAxML_bootstrap.boot RAxML_bootstrap.MRLresult
mv RAxML_bestTree.bestML RAxML_bestTree.MRLresult
cat RAxML_info.bestML RAxML_info.boot RAxML_info.MRLresult > tmp && mv tmp RAxML_info.MRLresult
fi
else #rapid bootstrap
echo -e "Computing $bsrep rapid bootstrap replicates using RAxML...\n"
if [[ $location == "1" ]]; then
raxmlHPC-PTHREADS -T $TORQUE_RESC_TOTAL_PROCS -f a -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n MRLresult -m BINCAT -p 1234 -x 1234 -N $bsrep
elif [[ $location == "2" ]]; then
raxmlHPC-PTHREADS-SSE3 -T $NSLOTS -f a -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n MRLresult -m BINCAT -p 1234 -x 1234 -N $bsrep
elif [[ $numbcores == "1" ]]; then
$raxmlseq -f a -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n MRLresult -m BINCAT -p 1234 -x 1234 -N $bsrep
else
$raxmlpthreads -T $numbcores -f a -s MRLmatrix_${MISSINGPERCENT}_${SPECIESPRESENCE}.phylip -n MRLresult -m BINCAT -p 1234 -x 1234 -N $bsrep
fi
fi
#Modify labels in RAxML bipartitions (XX and YY to ' ')
sed -i.bak 's/XX/-/g' RAxML_bipartitions.MRLresult
sed -i.bak 's/YY/_/g' RAxML_bipartitions.MRLresult
#(Re)root/rename a final MRL species tree with $OUTGROUP
if [ -n "$OUTGROUP" ]; then
nw_reroot -s RAxML_bipartitions.MRLresult $OUTGROUP > MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre
else
cp RAxML_bipartitions.MRLresult MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre
fi
#Modify labels in RAxML bipartitions (XX and YY to ' ')
sed -i.bak 's/-/ /g' MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre
sed -i.bak2 's/_/ /g' MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre
sed -i.bak3 's/e 0/e-0/g' MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre
#Delete all *.bak files
rm *.bak*
#Rename/delete files
mv RAxML_info.MRLresult RAxML_MRL_info.log
mv RAxML_bootstrap.MRLresult MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}_allbootstraptrees.tre
rm RAxML_bipartitionsBranchLabels.MRLresult
rm RAxML_bipartitions.MRLresult
rm RAxML_bestTree.MRLresult
#Rename MRL trees
if [[ $requisite =~ "yes" ]]; then
if [[ ! $collapse -eq "0" ]]; then
mrltree=MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}_with_requisite_collapsed${collapse}
else
mrltree=MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}_with_requisite
fi
else
if [[ ! $collapse -eq "0" ]]; then
mrltree=MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}_collapsed${collapse}
else
mrltree=MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}
fi
fi
#Copy results to home
if [[ $update =~ "yes" ]]; then
cp RAxML_MRL_info.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}MRL/${mrltree}_info.log
cp MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}_allbootstraptrees.tre $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}MRL/${mrltree}_allbootstraptrees.tre
cp MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/update/species_trees/${modif}MRL/${mrltree}.tre
else
cp RAxML_MRL_info.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}MRL/${mrltree}_info.log
cp MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}_allbootstraptrees.tre $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}MRL/${mrltree}_allbootstraptrees.tre
cp MRL_${MISSINGPERCENT}_${SPECIESPRESENCE}.tre $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}MRL/${mrltree}.tre
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}MRL
else
cp ${logname}.log $path/${treepath}${MISSINGPERCENT}_${SPECIESPRESENCE}/${tree}/species_trees/${modif}MRL
fi
#Clean scratch/work directory
if [[ $PBS_O_HOST == *".cz" ]]; then
#delete scratch
if [[ ! $SCRATCHDIR == "" ]]; then
rm -rf $SCRATCHDIR/*
fi
else
cd ..
rm -r workdir08c
fi
echo -e "HybPhyloMaker8c finished...\n"