*BEAST 2 + bModeltest doesn't work

[Thijs Janzen]

Dear beast-users,

I'm about to set up an analysis of 9 genes (3 mito, 6 nuclear), for ~80 species. 

Previously, I would use PartitionFinder to infer partitions and substitution models, and feed that to *BEAST. 

However, as *BEAST 2 has recently been released (which is faster), I would like to use *BEAST 2 now.

Furthermore, as I understand it, it is better to use a package such as bModeltest to infer substitution models. I could still use the partitions inferred by partitionFinder, or partition by gene type (e.g. all mito genes together, and the nuclear genes each separately), however, I would now simultaneously infer substitution models with my tree, which should provide more accurate results.

However, when setting up the analysis in BEAUti, I can not select bModeltest in the drop down menu under "site model", after creating a BEAUti session using either of the STARBEAST 2 templates (I'm mainly looking at SpeciesTree_UCLN, but I tested the other ones as well, and they don't work either).

It does appear when I use the template for StarBeast, so perhaps development of *BEAST 2 hasn't progressed towards including bModeltest yet?

Thanks in advance!

Thijs Janzen

[Carlo Pacioni]

Hi Thiis,
Just in case, have you installed the bmodeltest package?

Btw, I don't think the the analysis is necessarily more accurate, but it takes into account the uncertainty around the substitution model.

Cheers

---

From: Thijs Janzen
Sent: ‎2/‎02/‎2017 21:56
To: beast-users
Subject: *BEAST 2 + bModeltest doesn't work

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[Thijs Janzen]

Hi Carlo,

Yes, I did. When I start up the *BEAST template (not the *BEAST 2, but version 1), I do see the option to select bModeltest under "site Model". However, when starting a template of the *BEAST 2 suite, this option is not available.

Thijs

Op donderdag 2 februari 2017 12:47:09 UTC+1 schreef carlo pacioni:

[Huw A. Ogilvie]

Hi Thijs,

StarBEAST2 isn't yet compatible with bModelTest. I'll let you know when it is.

[Thijs Janzen]

Allright, supercool! (at least I'm not going crazy, and the option really isn't there :) )

I have no idea how complicated that it is to make them compatible - are we talking days / weeks / months? I'm happy to wait a bit, but the longer I wait, the less advantage the faster runtime of StarBEAST1 has ;)

Thanks in advance!

Thijs

Op donderdag 2 februari 2017 23:35:44 UTC+1 schreef Huw A. Ogilvie:

[Remco Bouckaert]

Hi Thijs,

If you update bModelTest to v1.0.2, it will be available in the StarBeast2 template.

Cheers,

Remco

[Thijs Janzen]

Hi Remco,

Many, many thanks! It works like a charm.

Thijs

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[Pedro Paulo Goulart Taucce]

Hi everyone,

Is StarBeast2 compatible with bModelTest yet? I am using BEAST 2.4.7 and the latest version of all packages and when I try to save using both it simply do not save. I have tried the same thing in both OSX 10.9.5 and Windows 10 and it didn't work.

Thanks in advance,

Pedro

[Huw A. Ogilvie]

Hi Pedro,

Yes bModelTest has been compatible with StarBEAST2 for about six months now. Do you mean no file is created? Is there any other weirdness in BEAUTi you can point to, like missing panels? Which particular StarBEAST2 template are you using?

- Huw

[Pedro Paulo Goulart Taucce]

Hello Huw,

Yes, no file is created. I don't think there is another weirdness. I am using StarBEAST2 template, the regular one.

Me. Pedro P. G. Taucce

Universidade Estadual Paulista "Júlio de Mesquita Filho" - UNESP

Instituto de Biociências

Departamento de Zoologia, Jacarezário

Av. 24 A, 1515, Bairro Bela Vista

Rio Claro - SP

CEP 13506-900

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[Huw A. Ogilvie]

Could you upload a screenshot of what BEAUTi looks like after you have changed the site model to BEAST model test?

[Pedro Paulo Goulart Taucce]

This is before I change:

This is after I change:

This is after I save:

Still don't get the resulting save file, it simply does not appear. I have tried on BEAST 2.4.6 in both OSX and Windows and BEAST 2.4.7 in Windows. It works fine with HKY.

Cheers,

Pedro

Me. Pedro P. G. Taucce

Universidade Estadual Paulista "Júlio de Mesquita Filho" - UNESP

Instituto de Biociências

Departamento de Zoologia, Jacarezário

Av. 24 A, 1515, Bairro Bela Vista

Rio Claro - SP

CEP 13506-900

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[Huw A. Ogilvie]

Hi Pedro,

This is really weird, and I can't replicate the results on my computer. If you save the HKY file, then close BEAUTi, and reopen it, can you change from HKY to BMT and save a new file? If not, can you send me the HKY XML and I will try to debug it.

- Huw

[Pedro Paulo Goulart Taucce]

Hi Huw,

I have opened the HKY file and then changed to BMT. It worked! Thanks a lot!

Pedro

Me. Pedro P. G. Taucce

Universidade Estadual Paulista "Júlio de Mesquita Filho" - UNESP

Instituto de Biociências

Departamento de Zoologia, Jacarezário

Av. 24 A, 1515, Bairro Bela Vista

Rio Claro - SP

CEP 13506-900

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[Pedro Paulo Goulart Taucce]

Hi Huw,

Actually it just worked once, and it printed an error message (attached). 

Then I have tried to change to bModelTest again it gave the following error:

And when I open de HKY file the population model tab looks like this:

I am attaching the stdout file and I will send you the hky input file.

Thank you very much for your time!

Me. Pedro P. G. Taucce

Universidade Estadual Paulista "Júlio de Mesquita Filho" - UNESP

Instituto de Biociências

Departamento de Zoologia, Jacarezário

Av. 24 A, 1515, Bairro Bela Vista

Rio Claro - SP

CEP 13506-900