BEAST2 and Pathsampling

[Marie]

Hi,

I run into this error message when trying to do a pathsampling analysis with my data, in BEAST2 using the "Pathsampler" package from the AppStore.

Error :  impossible to find or load the main class beast.app.beastapp.BeastMain

\tmp\step0\beast.xml.state (the specified file cannot be found)

What does it mean? What is the main class and why is it looking for a beast.xml.state file ?

Thanks a lot for your help,

Marie

[Remco Bouckaert]

Hi Marie,

The message indicates that there may be something wrong with the way the java path is set up, so it cannot find BeastMain any more.

Does the directory \tmp exist?

Which version of PathSampler are you using? Perhaps upgrading to the latest version may help. 

Cheers,

Remco

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[Marie]

The rootdir is set as C:\tmp which does exist and it seems to find it, as it's written : 

C:\Users\Marie\Desktop\Marie softwares\BEAST>cd "C:\tmp\step0"

But then : 

C:\tmp\step0\run.bat

C:\Users\Marie\Desktop\Marie softwares\BEAST>cd "C:\tmp\step0" 

C:\tmp\step0>java -cp "C:/Users/Marie/Desktop/Marie softwares/BEAST/AppStore.exe;C:/Users/Marie/Desktop/Marie softwares/BEAST./lib/launcher.jar;/C:/Users/Marie/BEAST/2.4/BEAST/lib/beast.jar;/C:/Users/Marie/BEAST/2.4/BEAST/lib/beast.src.jar;/C:/Users/Marie/BEAST/2.4/BEASTLabs/lib/BEASTlabs.addon.jar;/C:/Users/Marie/BEAST/2.4/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar;/C:/Users/Marie/BEAST/2.4/SA/lib/SA.addon.jar;/C:/Users/Marie/BEAST/2.4/substBMA/lib/substBMA.v1.2.2.jar;/C:/Users/Marie/Desktop/Marie softwares/BEAST/lib/beast.src.jar;/C:/Users/Marie/BEAST/2.4/BEAST/lib/beast.src.jar" beast.app.beastapp.BeastMain -overwrite -java -seed 176451196 beast.xml 

Erreur : impossible de trouver ou charger la classe principale beast.app.beastapp.BeastMain

C:\tmp\step0\beast.xml.state (Le fichier spécifié est introuvable)

Pathsampler version is 1.3.1, which I think is the newest (?)

Thanks a lot for your help,

Marie

[Marie]

And the "browse" is not working, so I tried putting my xml file in the BEAST folder and typing its name in the pathsampler window, but nothing's happening. I tried with the example files too, but same thing. 

I checked the versions of BEAST, Model selection package and beastlabs, and even JAVA, its all the newest. 

Would anybody have an idea of what could be wrong? I'm running out of ideas of things to try...

Thanks!

[Kevin Daly]

Not wanting to hijack Marie's problem, but I'm also having issues running PathSampler (running on ubuntu). When I click the "ok" button, having selected my xml file and left everything else at default, the dialog box closes. In the terminal window from which I launched beauti, I get the following: 

Exception in thread "main" java.lang.NoSuchMethodError: beast.app.util.ConsoleApp.<init>(Ljava/lang/String;Ljava/lang/String;Ljavax/swing/Icon;)V

at beast.app.tools.PathSampler.main(Unknown Source)

I also get the following message when PathSampler is being loaded from the app menu:

Loading package BEAST v2.4.1

Loading package BEASTLabs v1.5.3

Loading package MGSM v0.2.0

Loading package BEAST v2.4.1

Loading package MODEL_SELECTION v1.3.1

beast.util.XMLParserException: 

Error 1006 parsing the xml input file

nullCannot instantiate class. Please check the spec attribute.

Error detected about here:

  <beast>

      <subtemplate id='HyperPrior'>

          <connect>

at beast.util.XMLParser.createBeastObject(Unknown Source)

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseInputs(Unknown Source)

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseFragment(Unknown Source)

at beast.util.XMLParser.parseBareFragment(Unknown Source)

at beast.app.beauti.BeautiConfig.initAndValidate(Unknown Source)

at beast.app.tools.PathSampler.main(Unknown Source)

Any suggests would be great.

[Kevin Daly]

Like Marie, my /tmp directory exists. All versions of the apps are at their latest.

[Marie]

Ok, if everything (construction of xml file with Beauti + pathsampling analysis) is done in BEAST2.1.3 it works fine!

Is this a known issue of BEAST2.4 ? 

[Remco Bouckaert]

There appeared to be a problem with model selection v1.3.1 and BEASTLabs v1.5.3 interfering with each other. I released a new version for model selection (v1.3.2) and Marie and Kevin confirmed it solved the problem they encountered.

Remco