BEASTvntr Likelihood incorrectly calculated WARNING: Frequencies has wrong size. Expected 34, but got 4.

[amesclir]

Dear Arjun Dhawan,

This is my first time with BEASTvntr. I am having many troubles getting mydata set running.
First, I get a messsage "WARNING: Frequencies has wrong size. Expected 34, but got 4". I do not know how to fix this.
And the analyses crashes with this message "Likelihood incorrectly calculated".
You can see the whole message below.
Please, let me know how to contact you to send you the files. This is my email amesclir@gmail.com

Any thought could be helpful.
Thanks!
Cheers,
Marcial

File: helodes.xml seed: 1585830943910 threads: 1
Loading package bModelTest v1.2.1
Loading package SA v2.0.2
Loading package SNAPP v1.5.0
Loading package starbeast2 v0.15.5
Loading package BEASTvntr v0.1.3
Loading package MM v1.1.1
Loading package BEAST v2.6.2
Loading package BEASTLabs v1.9.2
Loading package BEAST v2.6.2
Alignment(mydata3aa)
70 taxa
33 sites
33 patterns

WARNING: Frequencies has wrong size. Expected 34, but got 4. Will change now to correct dimension and assume uniform distribution for initial values.
Using BEAGLE version: 3.2.0 (PRE-RELEASE) resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Using ambiguities in tree likelihood.
Ignoring character uncertainty in tree likelihood.
With 33 unique site patterns.
Using rescaling scheme : dynamic
Alignment(mydata3bb)
70 taxa
33 sites
33 patterns

Using BEAGLE version: 3.2.0 (PRE-RELEASE) resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Using ambiguities in tree likelihood.
Ignoring character uncertainty in tree likelihood.
With 33 unique site patterns.
Using rescaling scheme : dynamic

=================================================
Citations for this model:

Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne,
Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al.
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
PLoS computational biology 15, no. 4 (2019): e1006650.

Raazesh Sainudiin et al. (2004) Microsatellite Mutation Models.
Genetics 168:383-395

Chieh-Hsi Wu and Alexei J. Drummond. (2011) Joint Inference of
Microsatellite Mutation Models, Population History and Genealogies
Using Transdimensional Markov Chain Monte Carlo.
Genetics 188:151-164

===============================================================================
Start likelihood: -32192.51017277799
Warning: Overwriting file mydata3aa.log
Warning: Overwriting file Tree.trees
Sample posterior likelihood prior
0 -32191.4998 -32020.1506 -171.3492 --
2000 -6670.0626 -5937.4861 -732.5765 --
3000 -4051.6884 -3245.7550 -805.9333 --
4000 -3716.2548 -2948.5491 -767.7057 --
5000 -3581.0037 -2815.0593 -765.9443 --
6000 -3008.6556 -2254.0217 -754.6338 --
7000 3124.9009 3873.1857 -748.2847 --
8000 4043.5992 4801.0556 -757.4564 --
9000 6129.3312 6885.8061 -756.4748 --
10000 7098.8272 7853.0255 -754.1983 --
P(posterior) = 6975.571142958615 (was 7098.827207980195) **
P(prior) = -754.1983671222426 (was -754.1983671222426)
P(CoalescentConstant.t:Tree) = -741.2288563351107 (was -741.2288563351107)
P(biasMagnitudePrior.s:Site) = 0.0 (was 0.0)
P(focalPointPrior.s:Site) = -2.639057329615259 (was -2.639057329615259)
P(gPrior.s:Site) = 0.0 (was 0.0)
P(GammaShapePrior.s:Site) = -0.6843872375646877 (was -0.6843872375646877)
P(oneOnA1Prior.s:Site) = 0.0 (was 0.0)
P(PopSizePrior.t:Tree) = -9.646066219951983 (was -9.646066219951983)
P(likelihood) = 7729.769510080858 (was 7853.025575102438) **
P(treeLikelihood.mydata3aa) = -3744.2978001653305 (was -3744.2978001653305)
P(treeLikelihood.mydata3bb) = 11474.067310246188 (was 11474.067310246188)
At sample 10000
Likelihood incorrectly calculated: 7098.827207980195 != 6975.571142958615(123.25606502158007) Operator: Uniform(CoalescentConstantUniformOperator.t:Tree)
11000 7058.6719 7810.9683 -752.2963 6h30m57s/Msamples
12000 15447.7669 16250.4163 -802.6493 6h1m45s/Msamples
13000 16592.6066 17383.5492 -790.9426 5h47m35s/Msamples
14000 25572.7414 26354.0391 -781.2976 5h57m12s/Msamples
15000 35309.2893 36093.4556 -784.1663 5h49m3s/Msamples
16000 36258.9488 37014.1198 -755.1710 5h51m27s/Msamples

[arjun-1]

Hi @amesclir ,
Thank you for raising this issue. Unfortunately I'm no longer actively developing BEASTvntr, it's been a long time since I touched the code and am probably no longer comfortable with the statistical reasoning behind it 🙂 You should be able to conctact Remco Bouckaert, I believe he is still involved in the project

[amesclir]

Dear Arjun, Thank you much for the information. Cheers, Marcial El sáb., 11 abr. 2020 a las 11:59, Arjun Dhawan (<notifications@github.com>) escribió:

…

Hi @amesclir <https://github.com/amesclir> , Thank you for raising this issue. Unfortunately I'm no longer actively developing BEASTvntr, it's been a long time since I touched the code and am probably no longer comfortable with the statistical reasoning behind it 🙂 You should be able to conctact Remco Bouckaert, I believe he is still involved in the project — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACRWACW46LVESG5FGTPCVM3RMA5QPANCNFSM4MDXLLBA> .

-- A. Marcial Escudero Associate Professor Department of Plant Biology and Ecology Avda. Reina Mercedes 6 41012 Sevilla SPAIN Website: https://bit.ly/2oQzXkP Join us in the First Annual Symposium of Spanish Botany: https://bit.ly/2S87cL9