Eigenvector Negative Array Size Exception Error?

[Michael Johnston]

Hi,

I tried running eigenvector at 5 kb resolution and received the following error:

Exception in thread "main" java.lang.NegativeArraySizeException

at juicebox.matrix.InMemoryMatrix.<init>(InMemoryMatrix.java:50)

at juicebox.tools.clt.old.Pearsons.computePearsons(Pearsons.java:319)

at juicebox.data.MatrixZoomData.computePearsons(MatrixZoomData.java:571)

at juicebox.data.MatrixZoomData.getPearsons(MatrixZoomData.java:478)

at juicebox.data.Dataset.getEigenvector(Dataset.java:807)

at juicebox.tools.clt.old.Eigenvector.run(Eigenvector.java:149)

at juicebox.tools.HiCTools.main(HiCTools.java:86)

What could be causing this error?

Thanks for any tips!

- Michael

On a related note, the default juicer_tools script did not request enough memory to work with 5 kb resolution, leading to this error:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

at juicebox.data.MatrixZoomData.computePearsons(MatrixZoomData.java:549)

at juicebox.data.MatrixZoomData.getPearsons(MatrixZoomData.java:478)

at juicebox.data.Dataset.getEigenvector(Dataset.java:807)

at juicebox.tools.clt.old.Eigenvector.run(Eigenvector.java:149)

at juicebox.tools.HiCTools.main(HiCTools.java:86)

To allow it to run, the following change was made to the end of the juicer_tools script:

else # default, don't use temp directory or gpus, use CUDA 7.0

    # java -Djava.awt.headless=true  -Xmx16000m  -jar `dirname $0`/juicer_tools.jar  $*

    java -Djava.awt.headless=true  -Xmx32000m  -jar `dirname $0`/juicer_tools.jar  $*

fi

[Neva Durand]

Hello,

This means your matrices are too big to calculate the eigenvector at this resolution.  Java only allows ints to assign array lengths; the size of your matrix (dimension*dimension) is bigger than the maximum int (2,147,483,647) and so it's overflowing to a negative number.  

It's failing at line 50 in this file:

https://github.com/theaidenlab/juicebox/blob/master/src/juicebox/matrix/InMemoryMatrix.java

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Michael Johnston]

That makes perfect sense. Thank you!