BEAST runing- Error

[Masse T.]

Hi

I have beast installed on the HPC where I run my batch jobs, all I need to do it to load the module and run beast, packages model selection and SNAPP are also installed, I have modified the .xml file according to the documentation with minor changes:

<run spec='beast.inference.PathSampler'

chainLength="1000000"

alpha='0.3'

rootdir='/scratch/project_2001497/m20_outfiles/BEAST/m20-run1/'

burnInPercentage='50'

preBurnin="100000"

deleteOldLogs='true'

nrOfSteps='48'>

cd $(dir)

java -cp $(java.class.path) beast.app.beastapp.BeastMain $(resume/overwrite) -java -seed $(seed) beast.xml

 Now when running beast, I receive this error

Random number seed: 1580998515326

File: m20-run1.xml seed: 1580998515326 threads: 1

Loading package MODEL_SELECTION v1.5.2

Loading package BEASTLabs v1.9.1

Loading package SNAPP v1.5.0

Loading package BEAST v2.6.0

Loading package BEAST v2.6.0

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.math.distributions.Beta?

Perhaps a package required for this class is not installed?

Error detected about here:

  <beast>

      <run spec='beast.inference.PathSampler'>

          <mcmc id='mcmc' spec='MCMC'>

              <state id='state' spec='State'>

                  <stateNode id='Tree.m20' spec='beast.util.ClusterTree'>

                      <taxa id='snap.m20' spec='snap.Data'>

 

Does anyone know why?

[Masse T.]

I also tried to run an xml example in BEAST package, with the name testPathSamplerForSimpleTree.xml

I get an error for that too

java.lang.IllegalArgumentException: This BEASTInterface (beast.inference.PathSampler) has no input with name nrofsteps. Choose one of these inputs: alpha,nrOfSteps,rootdir,mcmc,chainLength,burnInPercentage,preBurnin,value,hosts,doNotRun,deleteOldLogs,posterior2prior

        at beast.core.BEASTInterface.getInput(Unknown Source)

        at beast.core.BEASTInterface.setInputValue(Unknown Source)

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

        at beast.util.XMLParser.createBeastObject(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)

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

        at java.lang.reflect.Method.invoke(Method.java:497)

        at beast.app.beastapp.BeastLauncher.run(Unknown Source)

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

Error 124 parsing the xml input file

This BEASTInterface (beast.inference.PathSampler) has no input with name nrofsteps. Choose one of these inputs: alpha,nrOfSteps,rootdir,mcmc,chainLength,burnInPercentage,preBurnin,value,hosts,doNotRun,deleteOldLogs,posterior2prior

Error detected about here:

  <beast>

      <run spec='beast.inference.PathSampler'>

seems like in both cases there is a problem with the; beast.inference.PathSampler

Any ideas please?

[Remco Bouckaert]

You can make it run by replacing “nrofsteps” by “nrOfSteps” — attribute names are case sensitive.

It looks like the file testPathSamplerForSimpleTree.xml comes with BEASTLabs, but should be in the model-selection package (probably a remnant of development in the past where I forgot to update this file, so I’ll move it there). 

Remco

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[Remco Bouckaert]

The error messages indicates BEAST cannot find a class from the SNAPP package. It is a bit of a mystery why that is, since the screen output shows that SNAPP v1.5.0 is loaded, which indicates the SNAPP package is installed and should be available. For some reason it is not. You could run a SNAPP analysis (without the path sampling bit, just MCMC) to confirm that it is the SNAPP installation that causes the problem.

Did you install the packages via the packagemanager utility that comes with BEAST? Perhaps removing the file ~/beast/2.6/beauti.properties may help reset the class path. Otherwise, removing the ~/.beast/2.6 folder and installing the SNAPP and MODEL_SELECTION package through the package manager may fix the problem.

Hope this helps,

Remco

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[Masse T.]

However, even by manually installing the BEASTlabs package as a separate subfolder, I receive this error which  I don't understand:

[Fatal Error] m20-run1.xml:348:3: The element type "beast" must be terminated by the matching end-tag "</beast>".

As I showed the script of my xml file in the previous message, the end tag IS  "</beast>" , so I don't understand where the problem is
p.s. (only mcmc analysis)

Remco

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[Masse T.]

Dear Remco,

Thanks for answering, I removed the pathsampler block of text and re-ran the beast, I receive the error of BEASTlabs not being installed in the package MODEL SELECTION, as you had guessed.

File: m20-run1.xml seed: 1581328967401 threads: 1

Package MODEL_SELECTION requires another package (BEASTLabs) which is not available.

Either uninstall MODEL_SELECTION or ask the package maintainer for information about this dependency.

Unexpected behavior may follow!

Loading package MODEL_SELECTION v1.5.2

Loading package SNAPP v1.5.0

Loading package BEAST v2.6.0

Loading package BEAST v2.6.0

[Fatal Error] m20-run1.xml:348:3: The element type "beast" must be terminated by the matching end-tag "</beast>".

java.lang.IllegalArgumentException: org.xml.sax.SAXParseException; systemId: file:/scratch/project_2001497/m20_outfiles/BEAST/m20-run1/m20-run1.xml; lineNumber: 348; columnNumber: 3; The element type "beast" must be terminated by the matching end-tag "</beast>".

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

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

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

        at java.lang.reflect.Method.invoke(Method.java:497)

        at beast.app.beastapp.BeastLauncher.run(Unknown Source)

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

Caused by: org.xml.sax.SAXParseException; systemId: file:/scratch/project_2001497/m20_outfiles/BEAST/m20-run1/m20-run1.xml; lineNumber: 348; columnNumber: 3; The element type "beast" must be terminated by the matching end-tag "</beast>".

        at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)

        at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:348)

        at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:205)

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

        ... 8 more

The packagemanager currently doesn't work in the supercluster system that I am connected to, so I have to download the zip file and install the packages as subfolders in /2.6/ manually, 

for your more information, that is how the begging and the end of the script in my .xml file look like now (after removing the path sampling)

I have also removed beauti.properties. 

now, should I delete and re-download packages again manually, if you have made some changes to them?

On Sunday, February 9, 2020 at 10:26:39 PM UTC+2, Remco Bouckaert wrote:

Remco

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[Remco Bouckaert]

The image suggests the run and mcmc elements are not balanced, so if you replace opening element

<mcmc

with

<run

and remove end element </mcmc> it may not cause this problem.

Remco