Not sure which package is missing for Error (cannot create class)

[Kavya Pradhan]

Hello BEAST-users,

I am currently trying to run bModelTest on my xml file that has two sequences for 673 species but I'm running into some trouble.
I originally tested a sample-species xml on a Mac OS and it worked fine, but because of the number of species decided it would be better to combine the results of several separate runs. So I have to now use a LINUX system.

I've looked around and it seems that often these kind of errors are associated with uninstalled packages but I keep getting the following error even though I have installed all the packages that were installed on the Mac 

java.lang.Exception: Class could not be found. Did you mean beast.math.distributions.Prior?

        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.parseInputs(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.parseRunElement(Unknown Source)

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

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

        at beast.app.BeastMCMC.parseArgs(Unknown Source)

        at beast.app.beastapp.BeastMain.main(Unknown Source)

Error 122 parsing the xml input file

Cannot create class: beast.math.distributions.BMTPrior. Class could not be found. Did you mean beast.math.distributions.Prior?

Error detected about here:

  <beast>

      <run id='mcmc' spec='MCMC'>

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

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

                  <distribution id='BMT_PropInvariantPrior.s:seq_matk_1' spec='beast.math.distributions.BMTPrior'>

The packages I have right now are:

 SA v1.1.3

 MSGM v0.1.3

 BEASTLabs v1.3.0

 RBS v1.2.2

 MODEL-SELECTION v1.1.0

 bModelTest v0.1.1

java version: 8
BEAST version 2.3.0

Any help would be much appreciated.

Thank you
Kavya

[Remco Bouckaert]

Hi Kavya,

The BMTPrior is part of the bModelTest package, so when you start BEAST it should report that it is loading that package like so:

Loading package bModelTest v0.1.1

If this message does not appear the package is not accessible. Note that when you install a package, by default it is only available for the user that installed it. If you run the job as another user (e.g. through a job queue), you need to install it again for that user, or you can install it for all users using the -useAppDir option to the addonmanager (see http://beast2.org/managing-packages/).

Cheers,

Remco

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[Kavya Pradhan]

Hi Remco,

Thank you for such a quick response.
I get a loading report that looks like this:

File: test_5_1_b.xml seed: 1435154545674 threads: 1

Loading package SA v1.1.3

Loading package MSGM v0.1.3

Loading package BEASTLabs v1.3.0

Loading package RBS v1.2.2

Loading package MODEL-SELECTION v1.1.0

Loading package bModelTest v0.1.1

Followed by the error message I posted above. All the packages are installed in my home directory so they should work. In fact, I was initially using the RBS package and it worked just fine.

Thank you
Kavya

[Kavya Pradhan]

For anyone who might have encountered the same problem, Remco helped me figure the issue out.

All you have to do is reinstall or update the RBS package to v1.2.4. After this all packages work great.

Thank you

Kavya