Problem relate to running ClueGO in Cytoscape

Question

[modarzi]

Hi, For Gene enrichment analysis, I used ClueGO as a Cytoscape plugin. At first, I updated ontologies.then, to enrichment analysis for my 40 Ensemble ids, I executed ClueGO in Cytoscape. The process will be continued but in the final stage for getting the GO network, my Cytoscape is closed suddenly. I have done this process but the results were similar.

My system and Cytscape Info:

Cytoscape Version: 3.7.2
ClueGO v2.5.6 + CluePedia v1.5.6
Java: 1.8.0_231 by Oracle Corporation Java 
Home: c:\program files\java\jre1.8.0_231 
OS: Windows 10 10.0 - amd64

I appreciated it if anybody guides me in this problem.

Best Regards,

Answer 1

[scooter]

If Cytoscape is closing, it means that something is crashing. There are two things you can try:

1. You could upgrade your Java to Java 11 (a much more current release) and your Cytoscape to 3.8, which is our latest. Note that Cytoscape works only with Java 11 (not Java 1.8, 12 or 13).
2. Alternatively, you could try to run Cytoscape from the command prompt and see what error is getting produced before it closes. That will help us to debug it.

-- scooter

[modarzi]

Hi, I upgrade my Cytoscape and that problem was solved. Thanks