BASTA Tutorial

[geo]

Dear All,

sorry or the stupid question.

Can somebody suggest me a tutorial to set up a BASTA analysis (as easily as possible :D )?

Thank you so much

Geo

[nicolad...@gmail.com]

Sorry in advance, it might be a bit outdated, but there is some instructions here:
https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/doc/BASTA_xml_file_guide.pdf
Let me know if that doesn't work!

Nicola

[geo]

Thank you so much!

I'll try it as soon as possible and let you know

Very best regards

Geo

[geo]

Dear Nicola,

I tried and  I get the following message:

File: TYLCV.xml seed: 1612943476299 threads: 1
Loading package CoupledMCMC v1.0.2
Loading package MultiTypeTree v7.0.2
Loading package BEAST v2.6.3
Loading package BEAST_CLASSIC v1.5.0
Loading package BASTA v3.0.1
Loading package phylodynamics v1.3.0
Loading package BDSKY v1.4.6
Loading package BEASTLabs v1.9.5
Loading package BEAST v2.6.3
Validation error when initializing object beast.evolution.tree.MigrationModelVolz (id null):
java.lang.IllegalArgumentException: Input 'nTypes' must be specified.
    at beast.core.Input.validate(Unknown Source)
    at beast.core.BEASTInterface.validateInputs(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)
    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:498)
    at beast.app.beastapp.BeastLauncher.run(Unknown Source)
    at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Error 110 parsing the xml input file

validate and intialize error: Input 'nTypes' must be specified.

Error detected about here:
  <beast>
      <run id='mcmc' spec='MCMC'>
          <init id='tree' spec='StructuredCoalescentMultiTypeTreeVolz'>
              <migrationModelVolz spec='MigrationModelVolz'>

I get the message with both my edited template and with the original TYLCV.xml file

I don't know if something changed in the BEAST2 package. I'm using  BEAST v2.6.3, 2002-2020

Thank you so much

Geo

[geo]

Probably I solved the problem by editing a little the XML

I'll see if it works on the long time and let you know!

[Danny Gustafson]

Good Morning All,

GEO - did you ever get BASTA to work with BEAST 2.6? I have not been able to even import the alignment, because the BASTA template give me a blank screen in BEAUti rather than the normal options. I am working on a structured coalescent analysis and would like to use the BASTA approximations rather than MultiTypeTree computationally intense approach. Thanks, Danny

PS. I am also working with Phylogeography on a Sphere Analysis, but I fear that ancient shared haplotypes across the species range is resulting in low ESS poterior values in this approach.

[nicolad...@gmail.com]

Hi Danny, I am afraid that the BASTA template will not work with BEAUti, but it would require editing the xml by hand as in 
https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/doc/BASTA_xml_file_guide.pdf

Best wishes,
Nicola