LG substitution Model in BEAST2

[Nicola Zadra]

Hi all, 

Using beast v2.5 by command line on both,  cluster and terminal (Linux laptop), I get an error:

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.evolution.substitutionmodel.WAG?

Perhaps a package required for this class is not installed?

Error detected about here:

  <beast>

      <run id='mcmc' spec='MCMC'>

          <distribution id='posterior' spec='util.CompoundDistribution'>

              <distribution id='likelihood' spec='util.CompoundDistribution'>

                  <distribution id='treeLikelihood.clear_Flavi_minor_Zika_al_full_beast' spec='ThreadedTreeLikelihood'>

                      <siteModel id='SiteModel.s:clear_Flavi_minor_Zika_al_full_beast' spec='SiteModel'>

                          <substModel id='LG.s:clear_Flavi_minor_Zika_al_full_beast' spec='LG'>

The packages needed are installed. 

Moreover, using ./beast instead beast.jar to launch the xml file, the run is working, what does it mean? why is  LG not working using the command line?

Best,

NIcola

 

[Remco Bouckaert]

Hi Nicola,

It looks like even though the package is installed, the package is not picked up. Did you install the package through BEAUti or the BEAST packagemanager? Perhaps the class path needs to be reset — you can do this in BEAUti using the menu File/Clear class path, or (more crudely) by deleting the ~/.beast/2.5/beauti.properties file.

If this does not help, what do you see on the terminal when you start with ./beast?

Cheers,

Remco

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[Nicola Zadra]

I tried to reset twice and I have installed the packages through both BEAUti and BEASt packagemanager, and is still not working.

This is what I see when I start beast with ./beast:

[/usr/lib/jvm/java-10-oracle/bin/java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib64:/lib64:/lib:/usr/lib, -cp, ::/home/lino/.beast/2.5/BEAST/lib/beast.jar:/home/lino/.beast/2.5/BEAST/lib/beast.src.jar:/home/lino/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/lino/.beast/2.5/BEAST_CLASSIC/lib/BEAST_CLASSIC.addon.jar:/home/lino/.beast/2.5/BEAST_CLASSIC/lib/mtj.jar, beast.app.beastapp.BeastMain]

BEAST v2.5.2, 2002-2019

Bayesian Evolutionary Analysis Sampling Trees

Designed and developed by

Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard  

do you have any raccomandation?

It seems to me that is just LGis not working because others runs that need packages are working well.

To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/80B9B1AA-0ACD-4CB0-80D9-44A80CEE1897%40gmail.com.

[Remco Bouckaert]

Thanks for following up — I tried to run an LG analysis with java 10 and BEAST ran fine.

What happens when you run this command from a terminal:

/usr/lib/jvm/java-10-oracle/bin/java -Xms8g -Xms256m -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib64:/lib64:/lib:/usr/lib -cp ::/home/lino/.beast/2.5/BEAST/lib/beast.jar:/home/lino/.beast/2.5/BEAST/lib/beast.src.jar:/home/lino/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/lino/.beast/2.5/BEAST_CLASSIC/lib/BEAST_CLASSIC.addon.jar:/home/lino/.beast/2.5/BEAST_CLASSIC/lib/mtj.jar beast.app.beastapp.BeastMain /path/to/yourfile.xml

where “/path/to/yourfile.xml” is the path to the XML file you want to run?

Cheers,

Remco

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