PathSampleAnalyser

[joan pons]

Dear Users,

I already ran path-sampling but I need to rerun 2 out of the 8 run.sh because they started at "infinite" value.

Can I delete output files for those two runs and rerun the run.sh again? Can I change the seed to avoid the "infinite" starting value?

If I get good results, how can I call  beast.inference.PathSampleAnalyser from terminal (beast 2.1.3) to estimate the marginal likelihood? I need the full path.

Thanks in advance,

Joan

[Remco Bouckaert]

Dear Joan,

Deleting the output files (*.log and *.trees) and rerunning through run.sh should be fine. However, if you have improper priors it is very well possible that you get infinities again, so you want to check your priors first.

To run the PathSampleAnalyser after the run is completed, assuming you are on Linux (which you had indicated before) and have BEAST installed in your home directory, from a terminal:

java -cp ~/BEAST/lib/beast.jar:~/.beast/2.1/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar beast.inference.

PathSampleAnalyser <nrOfSteps> <alpha> <rootDir> <burnInPercentage>

where <nrOfSteps> is 8 in your case, alpha, rootDir and burnInPercentage should be as specified in your XML file.

Hope this helps,

Remco

[Evan Wong]

Dear Joan and Remco,

I have a similar problem in that I need to re-estimate the marginal likelihood from the path sampling/stepping stone log files. The problem I have is that I cannot find the class "beast.inference.PathSampleAnalyzer". I have installed the model selection addon through beauti. However, in the BEAST program files there is no PathSampleAnalyzer file. When I look at the github website, I can see that there is an .inference package under beastii, however this cannot be downloaded. I do not know how to go about setting up a class for beast.inference.PathSampleAnalyzer because the files aren't available via the BEAST2 downloads or the github website. Am I looking in the wrong location for these files?

The error message that I end up getting is:
C:\Users\Evan>java -cp C:\Users\Evan\BEAST\lib\beast.jar:C:\Users\Evan\BEAST\2.1\MODEL_SELECTION\lib\MODEL_SELECTION.addon.jar beast.inference.PathSampleAnalyzer 8 0.3 C:Users\Evan\Desktop\Program_Files\BEST\BESAT\rootdir 0.1
Error: Could not find or load main class beast.inference.PathSampleAnalyzer

Any help would be great, thanks.

Evan Wong

[Remco Bouckaert]

Dear Evan,

Try British spelling :-)
  beast.inference.PathSampleAnalyser
instead of
  beast.inference.PathSampleAnalyzer

Remco

[Remco Bouckaert]

There is now a new release of the model-selection package v1.0.2 that allows you to run the PathSampleAnalyser using a graphical user interface instead of through a command line.

To use it:
- install model-selection package v1.0.2
- open the BEAST AppStore by double clicking its icon in the BEAST directory
- double click PathSampleAnalyser in the window that pops open.

There is a bit more detail here:
http://blog.beast2.org/2014/07/14/path-sampling-with-a-gui/

Remco

[Cuong trinh dinh]

Dear Ramco, 

I did as your way but i could not open the PathSampleAnalyser icon in appstore. Can you tell me what mistake did i meet?

Many thanks!

Dinh

Vào 22:01:53 UTC+2 Thứ hai, ngày 14 tháng bảy năm 2014, Remco Bouckaert đã viết:

[Remco Bouckaert]

Dear Dinh,

Did you install BEAST v2.1.3 with model-selection package v1.0.2?

The BEAST AppStore is inside the folder where you installed the BEAST package.

Cheers,

Remco

[Aron]

Dear Remco,

This does not seem to be working. BEAST v2.3.2, MODEL_SELECTION package v.1.1.3, on a mac. Also, when I manually edit the xml to run the PS/SS analysis, i get the following error:

/Users/aron/Desktop/pathsampling/step0/run.sh

File error: /Users/aron/Desktop/pathsampling/step0/beast.xml.state (No such file or directory)

Exception in thread "main" java.lang.UnsupportedClassVersionError: beast/app/beastapp/BeastMain : Unsupported major.minor version 52.0

at java.lang.ClassLoader.defineClass1(Native Method)

at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)

at java.lang.ClassLoader.defineClass(ClassLoader.java:621)

at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)

at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)

at java.net.URLClassLoader.access$000(URLClassLoader.java:58)

at java.net.URLClassLoader$1.run(URLClassLoader.java:197)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

at java.lang.ClassLoader.loadClass(ClassLoader.java:306)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)

at java.lang.ClassLoader.loadClass(ClassLoader.java:247)

However, the directory exists, and when I run the xml it adds folder & files to that directory. 

Help is always much appreciated, thanks!

Best,

Aron

[Graham]

In my experience, this message

Exception in thread "main" java.lang.

UnsupportedClassVersionError: beast/app/beastapp/BeastMain : Unsupported major.minor version 52.0

is a cryptic way of saying your Java version is too old. You need Java 8 for BEAST2.

[Aron]

I had Java 8, but I still updated Java, and still get the same error...

[Remco Bouckaert]

HI Aron,

It is possible you have multiple versions of java installed, including Java 8. You should make sure Java 8 is the default version used in the terminal: if you type

java -version 

from a terminal, it shows which version is the default version. You could remove older java versions, or if you need to keep them for because they are required by some programs, point that JAVA_HOME variable to the right place (more details here: http://superuser.com/questions/490425/how-do-i-switch-between-java-7-and-java-6-on-os-x-10-8-2).

Cheers,

Remco

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[Aron Katz]

Remco, Thanks! This worked!

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