Haploview CG limit error?
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8.6 years ago

I am following this tutorial on running GWAS analyses:

Basic statistical analysis in genetic case-control studies

doi:10.1038/nprot.2010.182

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

I used the gwas data found at http://www.well.ox.ac.uk/ggeu/NPanalysis/ 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?

java haploview gwas • 3.9k views
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7.8 years ago
ShirleyDai ▴ 50

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

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Unfortunately, no. :(

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7.6 years ago
alesssia ▴ 580

Hey,

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 http://stackoverflow.com/questions/1393486/error-java-lang-outofmemoryerror-gc-overhead-limit-exceeded). Try with this option: -XX:-UseGCOverheadLimit

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