java.lang.NullPointerException

[Luke Campillo]

Hey all,

Trying to get SNAPP to run on our cluster and I keep bumping into the same problem. Java. The cluster uses java 7 by default, but users are allowed to specify if they elect to use Java 8 instead, which I did. And that got Beast2 to load and I have enabled the SNAPP package. However once the MCMCs are about to start Java objects... And as you see, I am using Java 8, so I am not sure what the issue is. Any help would be greatly appreciated!!

Cheers,
Luke


Writing file Eury_1PP_A.1428339016313.log
         Sample      posterior ESS(posterior)     likelihood          prior
Writing file Eury_1PP_A.1428339016313.trees
Start state:
(((((0:0.10123383894843536,1:0.10123383894843536)6:0.021423240748593225,2:0.12265707969702859)7:0.027483926198352757,4:0.15014100589538135)8:0.030908067374153664,3:0.181049073269535)9:0.22538639724281878,5:0.4064354705123538)10:0.0
coalescenceRate[11 1] (-Infinity,Infinity): 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0
beta[1 1] (0.0,Infinity): 10.0
alpha[1 1] (0.0,Infinity): 2.0

Start likelihood: = -25149.085013082808
java.lang.NullPointerException
    at beast.core.MCMC.log(Unknown Source)
    at snap.MCMC.run(Unknown Source)
    at beast.app.BeastMCMC.run(Unknown Source)
    at beast.app.beastapp.BeastMain.<init>(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)
    at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Mon Apr 06 11:50:19 l133c586@n293:/scratch/l133c586/eury_SNAPP $ java -version
java version "1.8.0_31"
Java(TM) SE Runtime Environment (build 1.8.0_31-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode)
Mon Apr 06 11:50:36 l133c586@n293:/scratch/l133c586/eury_SNAPP $

[Remco Bouckaert]

Hi Luke,

Is it possible you set up the analysis with an older version of SNAPP? 

This problem is an issue that should be fixed in the current version of SNAPP (1.1.10).

Cheers, 

Remco 

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[Luke Campillo]

Remco,

I have SNAPP v1.1.10 installed... Any other ideas?

Cheers,
Luke

Wed Apr 08 10:14:34 l133c586@n099:/ $ addonmanager -list
Packages user path : /users/l133c586/.beast/2.2
Access URL : https://raw.githubusercontent.com/CompEvol/CBAN/master/packages2.2.0.xml
Getting list of packages ...Done!

Name : status : Description
BDSKY         (un-installed) : latest version 1.2.1 : birth death skyline - handles serially sampled tips, piecewise constant rate changes through time and sampled ancestors
BEAST_CLASSIC (un-installed) : latest version 1.1.8 : depends on BEASTlabs : BEAST classes ported from BEAST 1 in wrappers
BEASTlabs     (un-installed) : latest version 1.2.2 : BEAST utilities, such as multi threaded treeliklihood, Script
BEASTShell    (un-installed) : latest version 1.1.1 : BEAST Shell -- BeanShell scripting for BEAST
CA            (un-installed) : latest version 1.0.4 : CladeAge aPackage for fossil calibrations
DISSECT       (un-installed) : latest version 1.2.0 : Species delimitation with *BEAST
GEO_SPHERE    (un-installed) : latest version 0.0.5 : Whole world phylogeography
MASTER        (un-installed) : latest version 4.1.1 : Stochastic population dynamics simulation.
MGSM          (un-installed) : latest version 0.0.2 : Multi-gamma and relaxed gamma site models
MODEL_SELECTION (un-installed) : latest version 1.0.3 : Select models through path sampling/stepping stone analysis
morph-models (un-installed) : latest version 1.0.0 : Enables models of morphological chatacter evolution
MultiTypeTree (un-installed) : latest version 5.2.1 : Structured coalescent inference.
phylodynamics (un-installed) : latest version 1.1.0 : depends on BDSKY : birth death skyline model
RBS           (un-installed) : latest version 1.1.1 : Reversible-jump Based substitution model
SA            (un-installed) : latest version 1.1.2 : Sampled ancestor trees
SNAPP         (v1.1.10) : latest version 1.1.10 : SNP and AFLP Phylogenies
STACEY        (un-installed) : latest version 1.0.1 : Species delimitation and species tree estimation
SubstBMA      (un-installed) : latest version 1.1.2 : Substitution Bayesian Model Averaging
Wed Apr 08 10:14:43 l133c586@n099:/ $

[Remco Bouckaert]

Hi Luke,

Perhaps the XML file was created with an older version of SNAPP. You can simply edit the XML file in a text editor and replace

spec="snap.MCMC"

with

spec="beast.core.MCMC"

You may need to remove the stateBurnin attribute as well.

Cheers,

Remco

[Remco Bouckaert]

Hi Luke,

When BEAST is started without arguments, it indeed tries to open a window, which fails with the message you posted if there is no display.

Starting with the -help argument shows the list of arguments you can use — there is no argument for not using a display though.

What do you expect to happen if there is no display, and no arguments are given?

Cheers, Remco

On 9/04/2015, at 3:45 am, Luke Campillo <luke.ca...@gmail.com> wrote:

Remco,

Just another thought on what could be causing the problem (I am no expert haha just looking for anomalies). So if I just try to start BEAST without giving it an xml file, then I get an error about X11 DISPLAY not being set. As far as I can tell, the X11 enables the program to have a graphical interface. Which isn't really important to me at this stage in the analysis. I just want to use the badass computers on our cluster to get the data. When I want to see the output I can SCP to my desktop computer and open densitree on here.

So is there a way to tell BEAST I don't need to see any graphical output at this point? Like bypass the need for X11 to be set? Like I said, I am not an expert at all so I don't know if this is the problem... But it might be ;)

THANKS!
-Luke

####Error when loading BEAST w/o any xml input####

                           BEAST developers:
   Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled,
 Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
                 Oliver Pybus, Chieh-Hsi Wu, Walter Xie
                                   
                               Thanks to:
          Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207)
    at java.awt.Window.<init>(Window.java:536)
    at java.awt.Frame.<init>(Frame.java:420)
    at java.awt.Frame.<init>(Frame.java:385)
    at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(SwingUtilities.java:1758)
    at javax.swing.SwingUtilities.getSharedOwnerFrame(SwingUtilities.java:1833)
    at javax.swing.JOptionPane.getRootFrame(JOptionPane.java:1696)
    at javax.swing.JOptionPane.getWindowForComponent(JOptionPane.java:1637)
    at javax.swing.JFileChooser.createDialog(JFileChooser.java:802)
    at javax.swing.JFileChooser.showDialog(JFileChooser.java:749)
    at javax.swing.JFileChooser.showOpenDialog(JFileChooser.java:656)
    at beast.app.beastapp.BeastMain.getFileNameByDialog(Unknown Source)

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

Wed Apr 08 10:28:35 l133c586@n099:~ $

On Tuesday, April 7, 2015 at 1:35:02 PM UTC-5, Remco Bouckaert wrote: