java.lang.NullPointerException

[Renee Catullo]

Hi again,

I'm having some trouble getting SNAPP to run xml files. I've updated my computer to Java 8, and restarted my computer. However, when I run SNAPP, either with the xml I made, or the xml made here (http://www.peterbeerli.com/classes/index.php?title=BeastSNAPPTutorial), I get the following error:

java.lang.NullPointerException
at snap.util.TreeSetAnalyser.run(Unknown Source)
at snap.app.analysis.TreeSetAnalyser.<init>(Unknown Source)
at snap.app.analysis.TreeSetAnalyser.main(Unknown Source)

My student is also having this same error on both our and this tutorial xml files. I'm running OSX 10.11, and my java version is:

java version "1.8.0_111"
Java(TM) SE Runtime Environment (build 1.8.0_111-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode)

I have attached the tutorial xml file. Happy to provide my xml offline.

Cheers,

Renee

[Remco Bouckaert]

Hi Renee,

When you “run SNAPP” what you really should be doing is run BEAST with the SNAPP package installed. BEAST then produces a log and a tree file. SNAPP is known to be computationally expensive, so the log that is printed to screen may be quite slow — you can increase the log frequency by setting the logEvery attribute on the element with id=“screenlog” to something much lower than 1000 to get faster feedback. You may want to experiment with the number of threads to make BEAST run faster.

The TreeSetAnalyser that comes with the SNAPP package should only be used to analyse the tree file that BEAST produces.

Hope this clarifies things,

Remco

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<short.xml>

[Renee Catullo]

Hi Remco,

Thanks for that. I did think it weird that it was a tree set analyser.

Cheers,

Renee