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 )

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| | | ./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

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| | | 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.