Error 1017 parsing the xml input file ---BEAST v 2.6.1

[George Gao]

Hi all,

With BEAST v2.6.1 and the packages SA, MM, and BEASTLabs installed on a Linux server, I run a dataset and found an error as follows:

--------------------------------------------

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.evolution.sitemodel.SiteModel?

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='prior' spec='util.CompoundDistribution'>

                           <distribution id='FBD.t:tree' spec='beast.evolution.speciation.SABirthDeathModel'>

...

--------------------------------------------

I followed the suggestion of deleting beauty.properties file in ~/.beast/2.6/. However, it still didn't work. On the contrary, it appeared to work well for datasets which are not dependent on the packages such as ~/examples/testGTR.xml, and my dataset can run well on my laptop.

Any advice will be appreciated.

Cheers,

George Gao

[Remco Bouckaert]

Hi George,

Can you check in the screen output which package are loaded? If the SA package is properly installed (and is in the ~/.beast/2.6/SA directory, so there should be a file ~/.beast/2.6/SA/lib/SA.v2.0.2.jar depending on the installed version), it should show something like

...

Random number seed: 1572912535315

File: beast.xml seed: 1572912535315 threads: 1

Loading package BEAST v2.6.1

Loading package SA v2.0.2

…

just after the header. If the SA package is not picked up, but is available in ~/.beast/2.6/SA it may be because there is an issue with the BEAST package path. You can set the BEAST package path as an environment variable to force it to look at where the package is installed by setting the BEAST_PACKAGE_PATH on Linux like so

export BEAST_PACKAGE_PATH=/home/<yourname>/.beast/2.6

where <yourname> is your user name.

Hope this helps,

Remco

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[George Gao]

Hi Remco,

Thanks very much for your suggestions!

You are right. I have confirmed that it was due to the incomplete SA package I downloaded manually. The software now works very well.

Cheers,
George

[Yeserin YILDIRIM]

Hi Remco,

I have the same problem.  Trying to run snapper. Prepared the input file using  snapp_prep.rb.

 This is the error:

--

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.core.MCMC?

Perhaps a package required for this class is not installed?

Error detected about here:
  <beast>
      <run id='mcmc' spec='MCMC'>

--

That line in my xml file looks fine to me:

<run id="mcmc" spec="MCMC" chainLength="5000000" storeEvery="2500">

Below is how my slurm file looks like. The packages seem to be loaded. The prgram runs when I ran snapp, but I have this problem with snapper file. 

What could be the problem? I will appreciate your help a lot.

Best,
Yeserin.

File: snapper.xml seed: 777 threads: 16
Loading package BEAST v2.6.3
Loading package BEASTLabs v1.9.6
Loading package Babel v0.3.2
Loading package bacter v2.2.3
Loading package BADTRIP v1.0.0
Loading package BASTA v3.0.1
Loading package BDMM v1.0
Loading package MultiTypeTree v7.0.2
Loading package MASTER v6.1.2
Loading package BDSKY v1.4.6
Loading package BEAST_CLASSIC v1.5.0
Loading package BEASTvntr v0.1.3
Loading package Beasy v0.0.2
Loading package besp v0.2.0
Loading package bModelTest v1.2.1
Loading package BREAK_AWAY v1.0.0
Loading package GEO_SPHERE v1.3.0
Loading package CA v2.0.0
Loading package CoalRe v0.0.5
Loading package CodonSubstModels v1.1.3
Loading package CoupledMCMC v1.0.2
Loading package DENIM v1.0.0
Loading package SA v2.0.2
Loading package EpiInf v7.5.2
Loading package FastRelaxedClockLogNormal v1.1.1
Loading package feast v7.5.3
Loading package flc v1.1.0
Loading package Mascot v2.1.2
Loading package MGSM v0.3.0
Loading package MM v1.1.1
Loading package MODEL_SELECTION v1.5.3
Loading package MSBD v1.1.5
Loading package NS v1.1.0
Loading package ORC v1.0.2
Loading package outercore v0.0.6
Loading package PhyDyn v1.3.7
Loading package phylodynamics v1.3.0
Loading package PIQMEE v1.0.2
Loading package PoMo v1.0.1
Loading package SCOTTI v2.0.1
Loading package SNAPP v1.5.1
Loading package snapper v1.0.0
Loading package SpeciesNetwork v0.13.0
Loading package SSM v1.1.0
Loading package STACEY v1.2.5
Loading package starbeast2 v0.15.13
Loading package substBMA v1.2.3
Loading package TreeStat2 v0.0.2
Loading package TMA v1.0.0
Loading package BEAST v2.6.3

Error 1017 parsing the xml input file......

[felip...@gmail.com]

I ran into the same error when I prepared my xml file with snapp_prep.rb to run on BEAST 2.7.x.. which version are you using? not sure what's the problem but it worked for me when I ran the .xml file in BEAST 2.6.7 though.