Error 1017: Class could not be found when running BEAST with generated XML

[CamilaDuitama]

Description:

I encountered an error (1017) when trying to run BEAST with an XML file generated using the beast2-xml.py script. The error message suggests a missing class or package:

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.base.inference.MCMC?
Perhaps a package required for this class is not installed?

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

Steps to Reproduce:

1. Generate XML file using the command:

   beast2-xml.py --fastaFile all_dengue_aligned.fasta > output.xml

2. Run BEAST using the generated XML:

   beast output.xml

Environment:

• BEAST version: 2.7.3
• Operating System: Linux
• Input file: all_dengue_aligned.fasta

[terrycojones]

@CamilaDuitama thanks for the report. Could you try editing the XML file and changing that line to

<run id='mcmc' spec='beast.base.inference.MCMC'>

and trying to run beast2 again? That seems to be what the error message is suggesting. @m-d-grunnill may know more (I don't even use beast :-))

[CamilaDuitama]

No, this only generated another error:

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.base.evolution.tree.TraitSet?
Perhaps a package required for this class is not installed?

Error detected about here:
  <beast>
      <run id='mcmc' spec='beast.base.inference.MCMC'>
          <state id='state'>
              <tree id='Tree.t:alignment' name='stateNode'>
                  <trait id='dateTrait.t:alignment' spec='beast.evolution.tree.TraitSet'>

[m-d-grunnill]

@CamilaDuitama I would check that the minor version of beast in the template xml and the beast 2 minor version that you intend to run the xml on are the same. I have had issues with beast 2.6 not liking beast 2.7 xmls (possibly visa versa to). This a bit annoying.

I am stuck with 2.6 as I can only get BEAST 2 via conda for the HPC I work with.

[CamilaDuitama]

So here is the XML file I obtained from using beast2-xml.py. I notice it retains version="2.4" by default. If I change it to version 2.7, I still receive the same error.

Can I run beastv2.7.3 with the output of this script? Can I run BEAST X v10.5.0-beta4?

output.xml