diff --git a/JolyTree.sh b/JolyTree.sh
index 0dcf55e6207840fd4a69b43fce72b3ecc7257b91..362a8315a8d476f07dab09c6bf1bf3e440ac0beb 100755
--- a/JolyTree.sh
+++ b/JolyTree.sh
@@ -4,7 +4,7 @@
# #
# JolyTree: fast distance-based phylogenetic inference from unaligned genome sequences #
# #
- COPYRIGHT="Copyright (C) 2017-2020 Institut Pasteur" #
+ COPYRIGHT="Copyright (C) 2017-2021 Institut Pasteur" #
# #
# This program is free software: you can redistribute it and/or modify it under the terms of the GNU #
# General Public License as published by the Free Software Foundation, either version 3 of the License, or #
@@ -33,7 +33,13 @@
# = VERSIONS = #
# ============ #
# #
- VERSION=2.0.190926ac #
+ VERSION=2.1.211019ac #
+# + commenting line 576, as some linux distribution incorrectly interpret "trap [arg] signal_spec" with #
+# empty arg #
+# + adding some conditions to deal with some FastME crashes observed when inferring large trees #
+# + new option -x to prevent
+# #
+# VERSION=2.0.190926ac #
# + new F81/EI transformation formula using gamma shape parameter (option -a = 1.5 by default) #
# + option -f to to use the 4 nucleotide frequencies in F81/EI transformation; by default, to deal with #
# multiple contig files, JolyTree sets f(A)=f(T)=0.5*(A+T)/(A+C+G+T) and f(C)=f(G)=0.5*(C+G)/(A+C+G+T) #
@@ -95,6 +101,10 @@
Criscuolo A (2019) A fast alignment-free bioinformatics procedure to infer accurate
distance-based phylogenetic trees from genome assemblies. RIO. doi:10.3897/rio.5.e36178
+ Criscuolo A (2020) On the transformation of MinHash-based uncorrected distances into
+ proper evolutionary distances for phylogenetic inference. F1000Research.
+ doi:10.12688/f1000research.26930.1
+
USAGE: JolyTree.sh -i <directory> -b <basename> [options]
OPTIONS:
@@ -117,6 +127,7 @@
-n no BME tree inference (only pairwise distance estimates)
-r <int> number of steps when performing the ratchet-based BME tree search
(default: 100)
+ -x no branch support
-t <int> number of threads (default: 2)
EOF
@@ -249,11 +260,13 @@ INFERTREE=true; # -n (none)
RATCHET=100; # -r (100)
RATCHET_LIMIT=200; # (static)
+BRANCH_SUPPORT=true; # -x (none)
+
NPROC=2; # -t (2)
CHUNK=20; # -h (20)
WAITIME=0.5; # (auto from -t)
-while getopts :i:b:s:q:k:c:a:d:r:t:h:nf option
+while getopts :i:b:s:q:k:c:a:d:r:t:h:nfx option
do
case $option in
i) DATADIR="$OPTARG" ;;
@@ -265,6 +278,7 @@ do
a) ALPHA="$($GAWK -v x=$OPTARG 'BEGIN{printf "%.20f", x+0}' | sed 's/0*$//g')" ;;
f) NFQ=4 ;;
n) INFERTREE=false ;;
+ x) BRANCH_SUPPORT=false ;;
r) RATCHET=$OPTARG ;;
h) CHUNK=$OPTARG ;;
t) NPROC=$OPTARG ;;
@@ -559,7 +573,7 @@ if ! $INFERTREE ; then exit 0 ; fi
#############################################################################################################
#############################################################################################################
-trap INT ;
+# trap INT ;
function ctrl_c() {
echo -n " process interrupted: deleting files ... " ;
sleep 5 ;
@@ -588,8 +602,14 @@ OUTTREE=$BASEFILE.tt;
$FASTME -i $DMAT -o $OUTTREE -s -f 12 -T 1 &> /dev/null ;
tblo=$(grep -B1 "Performed" $BASEFILE.dd_fastme_stat.txt | sed -n 1p | sed 's/.* //g' | sed 's/\.$//g');
[ -z "$tblo" ] && tblo=$(grep -o ":[0-9\.-]*" $OUTTREE | tr -d :- | paste -sd+ | bc -l | sed 's/^\./0./');
-echo " step 0 $tblo" >&2 ;
-echo "step 0 tbl=$tblo" ;
+if [ -z "$tblo" ]
+then
+ tblo=999999;
+ echo " step 0 NaN" >&2 ;
+else
+ echo " step 0 $tblo" >&2 ;
+ echo "step 0 tbl=$tblo" ;
+fi
cp $OUTTREE $BMETREE;
sed -f $TAXFILE $BMETREE > $BMETREE.tmp ; mv $BMETREE.tmp $BMETREE ; # <=> sed -f $TAXFILE -i $BMETREE ;
rm -f $BASEFILE.dd_fastme_stat.txt ;
@@ -615,7 +635,7 @@ then
END {print" "n;i=0;while(++i<=n){printf lbl[i];j=0;while(++j<=n){printf(" %.8f",d[i][j])}print""}}' $DMAT.$x.c > $DMAT.$x.n ;
### ratchet-search tree search ########################################################################
- $EXEC "$FASTME -i $DMAT.$x.n -u $OUTTREE -o $OUTTREE.$x.n -nB -s -T 1 ; sed 's/:-/:/g' $OUTTREE.$x.n > $OUTTREE.$x.m ; $FASTME -i $DMAT.$x.c -u $OUTTREE.$x.m -o $OUTTREE.$x.c -s -T 1 ; rm -f $DMAT.$x.n $DMAT.$x.m $DMAT.$x.n_fastme_stat.txt $OUTTREE.$x.n $OUTTREE.$x.m ;" &> /dev/null &
+ $EXEC "$FASTME -i $DMAT.$x.n -u $OUTTREE -o $OUTTREE.$x.n -nB -s -T 1 ; sed 's/:-/:/g' $OUTTREE.$x.n > $OUTTREE.$x.m ; $FASTME -i $DMAT.$x.c -u $OUTTREE.$x.m -o $OUTTREE.$x.c -s -T 1 -f 12 ; rm -f $DMAT.$x.n $DMAT.$x.m $DMAT.$x.n_fastme_stat.txt $OUTTREE.$x.n $OUTTREE.$x.m ;" &> /dev/null &
done
while [ $(jobs -r | wc -l) -gt 0 ]; do sleep $WAITIME ; done
@@ -629,8 +649,9 @@ then
rm -f $DMAT.$x.c_fastme_stat.txt ;
out=" ";
[ -z "$tbl" ] && tbl=$(grep -o ":[0-9\.-]*" $OUTTREE.$x.c | tr -d :- | paste -sd+ | bc | sed 's/^\./0./') && out="+";
+ [ -z "$tbl" ] && tbl="NaN";
echo -n "$out step $step_prev $tbl" >&2 ;
- if [ $(echo "$tbl<$tblo" | bc) -eq 0 ]
+ if [ "$tbl" == "NaN" ] || [ $(echo "$tbl<$tblo" | bc) -eq 0 ]
then
rm -f $OUTTREE.$x.c ;
echo " (epsilon=$v)" >&2 ;
@@ -655,13 +676,18 @@ fi
#############################################################################################################
#############################################################################################################
-echo -n "estimating branch supports ... " >&2 ;
-$REQ $BASEFILE.d $BMETREE $OUTTREE ;
-echo "[ok]" >&2 ;
-mv $OUTTREE $BMETREE ;
-echo "BME tree (tbl=$tblo) with branch supports written into $BMETREE" ;
-rm -f $DMAT $TAXFILE $OUTTREE ;
+if $BRANCH_SUPPORT
+then
+ echo -n "estimating branch supports ... " >&2 ;
+ $REQ $BASEFILE.d $BMETREE $OUTTREE ;
+ echo "[ok]" >&2 ;
+ mv $OUTTREE $BMETREE ;
+ echo "BME tree (tbl=$tblo) with branch supports written into $BMETREE" ;
+else
+ echo "BME tree (tbl=$tblo) written into $BMETREE" ;
+fi
+rm -f $DMAT $TAXFILE $OUTTREE ;
exit ;