BUG: LSD Phylogenetic Dating does not output any result

[Gipsy-The-Sheller]

Dear developers,

my iq-tree 3 version is:

IQ-TREE version 3.0.1 for Windows 64-bit built May  5 2025

downloaded from the official website of iqtree.

I'm now attempt to do molecular dating for a set of simulated sequences by evolver:

>A
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
>B
TTTTTTTTTTTTTTTCCCCCCCCCCAAAAAAAGGGGGGTTTTTTTTTTTTCCCCCCCCCCCCAAAAAAAAAGGGGGGGGTTTTTTTTTTCCCCCCCCCCAAAAAAAAAAGGGGGGGGGGTTTTTTTTTTCCCCCCCAAAAAAAAAGGGGGGGGGGGGGG
>C
TTTTCCCCAAAGGGGTTCCCCAAGGTCCAGGGTCCAGGTTTCCCAAGGGGTTTCCCCAAGGGTTCCCAAAGTTTCCAAGTTTCCCAAGGTTTTCCCAAGTTCCAAAGGGTTTCCCAAGGTTTCCAAGGGTTCCAGGTTTCCCAAGTTCCCCAAAAGGGG
>D
TCAGTCAGTCATCAGTCTCAGAGCGTTCACAGTTCATGTAGTCACATCAGTCGTCAGCATCGTGTCGCAGGTCATCAGGTCATCATATATCAGTCATAGTATCTAGCAGTCGCAGTAAGTAGCACATCGTACGCCGTCATCGAGGTGTCAGTCAGTCAG

My command is:

$ iqtree3 -s md.fas --date md.date --date-tip 0 -redo

in which the date file is:

A,B -100
C,D -50

However, LSD did not generate any output:

Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
-a----          2026/2/1     15:06              0 evolver.out
-a----          2026/2/1     15:11           1589 mc.txt
-a----          2026/2/1     15:11            123 MCbase.dat.tmp
-a----          2026/2/1     15:14             17 md.date
-a----          2026/2/1     15:13            660 md.fas
-a----          2026/2/1     15:24             67 md.fas.bionj
-a----          2026/2/1     15:24            721 md.fas.ckp.gz
-a----          2026/2/1     15:24          26358 md.fas.iqtree
-a----          2026/2/1     15:24          26932 md.fas.log
-a----          2026/2/1     15:24            215 md.fas.mldist
-a----          2026/2/1     15:24           4050 md.fas.model.gz
-a----          2026/2/1     15:24             79 md.fas.treefile
-a----          2026/2/1     15:06             12 SeedUsed

I tried the phylogenetic dating function of IQ-Tree 2 on Galaxy with the same data, and it output a timetree:

#NEXUS
Begin trees;
tree 1 = ((C[&date="1.25916e+10"]:1.25916e+10,D[&date="27661"]:27711)[&date="-50"]:8.02829e+09,(A[&date="6.10993e+09"]:6.10993e+09,B[&date="1.15995e+10"]:1.15995e+10)[&date="-100"]:8.02829e+09)[&date="-8.02829e+09"];
End;

Should I switch to a new release? Or will this be fixed later?

Thanks.

[Gipsy-The-Sheller]

Then I tried iq-tree v2.2.0, which printed the LSD log and output dated chronogram:

--- Start phylogenetic dating ---
Reading date file md.date ...
2 dates extracted
Building time tree by least-square dating (LSD) with command:
lsd -i md.fas.timetree.subst -s 159 -o md.fas.timetree -r a -d md.fas.timetree.date -z 0

TREE 1
*PROCESSING:
Reading the tree ...
Collapse 0 (over 1) internal branches having branch length <= 0.00314
 (settable via option -l)
Parameter to adjust variances was set to 1.16 (settable via option -b)
Minimum branch length of time scaled tree (settable via option -u and -U): 0
Estimating the root position on all branches using fast method ...

*RESULTS:
- Dating results:
 rate 0.00840769, tMRCA -170.486 , objective function 0.516899

TOTAL ELAPSED TIME: 0.013 seconds
LSD results written to:
  LSD report:                  md.fas.timetree.lsd
  Time tree in nexus format:   md.fas.timetree.nex
  Time tree in newick format:  md.fas.timetree.nwk

--- End phylogenetic dating ---
Date and Time: Sun Feb 01 15:33:48 2026