phytime not working on the dating_example.xml

[Jigyasa3]

Hey!

I am testing the phytime run on the example file, and I get the following error-

code-
phytime --xml=dating_example.xml

error-
`
. 1365 patterns found (out of a total of 4533 sites).

. 3075 sites without polymorphism (67.84%).

. Starting tree: BioNJ

. Processing 1 data set ( ./seq.txt )

---

| |
| ./seq.txt (partition element 0) |
|_______________________________________________________________________|

. Number of rate classes: 3
. Model of rate variation: FreeRates
. Relative average rate: 1.000000

. Mixture class 1
Relative substitution rate: 1.714286
Rel. rate freq. (> 0 rates): 0.333333
Rate class number: 0
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: yes
Rate matrix weight: 1.000000
Optimise nucleotide freq.: no
Equ. freq. weight: 1.000000

. Mixture class 2
Relative substitution rate: 0.857143
Rel. rate freq. (> 0 rates): 0.333333
Rate class number: 1
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: yes
Rate matrix weight: 1.000000
Optimise nucleotide freq.: no
Equ. freq. weight: 1.000000

. Mixture class 3
Relative substitution rate: 0.428571
Rel. rate freq. (> 0 rates): 0.333333
Rate class number: 2
Substitution model: HKY85
Value of the ts/tv ratio: 4.000000
Optimise ts/tv ratio: yes
Rate matrix weight: 1.000000
Optimise nucleotide freq.: no
Equ. freq. weight: 1.000000

---

| |
| Model summary table |
|_______________________________________________________________________|

---

Partition element 0 0 0

State frequencies a a a
Branch lengths a a a
Rate matrix a a a

. Computing pairwise distances...

. Building BioNJ tree...

.......................................................................
Calibration id: cal1.
Lower bound set to: 40.000000 time units.
Upper bound set to: 60.000000 time units.
This calibration applies to node 28 with probability 0.8.
.......................................................................
Calibration id: cal1.
Lower bound set to: 40.000000 time units.
Upper bound set to: 60.000000 time units.
This calibration applies to node 25 with probability 0.2.
.......................................................................
Calibration id: cal2.
Lower bound set to: 50.000000 time units.
Upper bound set to: 200.000000 time units.
This calibration applies to node 28 with probability 1.
.......................................................................

. Is asynchronous: no
. upper: 0.000000 lower: 67.767593 t_mrca: 67.767593
phytime: times.c:1537: TIMES_Connect_List_Of_Taxa: Assertion FALSE' failed. Aborted (core dumped)

[stephaneguindon]

I'm sorry I do not have much time these days to look into this. I'll try my best next week but in the meantime I suggest
you use an older release.
Regards,
-Stephane-

[Jigyasa3]

Thanks for replying! I will use the older version.