Problems with Species Delimitation Analyser (STACEY, DISSECT)

[Melina]

Hi everybody, 

I´m new Stacey analysis user and I downloaded the Species Delimitation Analyser from its page, but It is not working in my computer (OS 10.7) or in virtual machine (Win XP).

Is there another method to run this?

Thanks in advance

Mel

[Graham]

Some more detail about what "not working" means might help.

If you can run BEAST1, you could try replacing

java  -jar speciesDA.jar

with
java -classpath <java.classpath> dr.app.tools.SpeciesDelimitationAnalyser
in the command line. <java.classpath> needs to be replaced with something which depends on your OS and where you installed BEAST1. In Windows it is something like
.;BEASTDIRECTORY;BEASTDIRECTORY\lib\*

Graham Jones

[Kunal Arekar]

Hi Graham

I tried running speciesDA in command prompt, but is shows the following error, "Unable to access jarfile speciesDA.jar". Is there a step by step guide to run this program? That will be really helpful.
I am not from computation background, so I have no idea how to troubleshoot this.

All help is appreciated

Thank you

[Cynthia Asorey]

Hi Kunal. ¿What OS are you using? speciesDA has problems when it is running under Mac OS because it has problem with java

Mel

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[Huw A. Ogilvie]

In general problems with Java in MacOS can be addressed by downloading and installing the latest JDK from directly from Oracle - http://www.oracle.com/technetwork/java/javase/downloads/index.html

[Graham]

I don't know what caused the error. If you put "Unable to access jarfile" into a search engine, you'll find some suggestions. (This is how 'experts' troubleshoot things they don't understand.)

Graham

[Kunal Arekar]

Thanks everyone for the inputs. I figured out the problem, the path was wrong.
@Melina, I use windows OS.

I have another issue though; how to visualise the clustering file? and what software to use for preparing the similarity matrix?

Kunal

[Graham]

Glad you got it working. There is an example R script for making a similarity matrix in the supplementary material of the DISSECT paper. You can also download from http://www.indriid.com/workingnotes2014.html.

Graham