Question: Haploview CG limit error?
gravatar for areyoujokingme
4.2 years ago by
United States
areyoujokingme60 wrote:

I am following this tutorial on running GWAS analyses: 

Basic statistical analysis in genetic case-control studies



(you will need probably academic access to Nature so you don't have to buy the article).


I used the gwas data found at and followed the instructions dutifully.


When I go to plot the Manhattan plot, however, I get a Java GC limit error. Specifically the error message reads:

"Fatal Error: Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded"


I can't tell if this is a Java error, or a Haploview error. I added the following Java parameter when I launched Haploview, to increase the max heap size allocated to Haploview, but it did not help.

java -jar -Xmx2048M Haploview.jar

Any thoughts?

haploview java gwas • 2.2k views
ADD COMMENTlink modified 3.3 years ago by alesssia550 • written 4.2 years ago by areyoujokingme60
gravatar for ShirleyDai
3.5 years ago by
ShirleyDai40 wrote:

Hi, Have you solved the problem? I am encountering the same error.

ADD COMMENTlink written 3.5 years ago by ShirleyDai40

Unfortunately, no. :(

ADD REPLYlink written 3.3 years ago by areyoujokingme60
gravatar for alesssia
3.3 years ago by
London, UK
alesssia550 wrote:


it is a Java error, but it is not a heap size problem: it is an issue of the garbage collector (GC). Specifically, "this message means that for some reason the garbage collector is taking an excessive amount of time (by default 98% of all CPU time of the process) and recovers very little memory in each run (by default 2% of the heap)." (see Try with this option: -XX:-UseGCOverheadLimit

ADD COMMENTlink written 3.3 years ago by alesssia550
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