MLM error in matrix math; does not occur for all chromosomes, or all datasets

[Ginnie M]

Hi,
I have the most recent (feb 4 2016) tassel5 build and am getting an error I'm not sure about for four of the ten maize chromosomes (no obvious pattern; chrm 1,4,5,6 fail). The errors are the same. From a very quick look at the chromosomes, there doesn't seem to be anything that sticks out as to why those chromosomes are getting the error. This error also was occurring with the Dec. 10 version, but does NOT occur with a different hmp file I was previously playing with. Any tips as to where to look for an error on my part would be appreciated.
 
As an example:
Tassel Pipeline Arguments: -debug -fork1 -h default_S1.hmp.txt -separate 4 -fork2 -t Tassel_S1.txt -fork3 -q S1_PCA_no01.txt -fork4 -k K_S1_IBS_no0.txt -combine5 -input1 -input2 -input3 -intersect -combine6 -input5 -input4 -mlm -mlmVarCompEst P3D -mlmCompressionLevel Optimum -export S1_IBS_chr4_ -runfork1 -runfork2 -runfork3 -runfork4
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.20  Date: February 4, 2016
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 58254 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_65
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 24

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[Thread-14] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.association.WeightedMLMPlugin  Citation: Shang Xue, Zachary Miller, Janu Verma,  First Annual Tassel Hackathon
[Thread-14] ERROR net.maizegenetics.plugindef.AbstractPlugin - 0
[Thread-14] INFO net.maizegenetics.plugindef.AbstractPlugin -
Usage:
WeightedMLMPlugin <options>

[Thread-14] DEBUG net.maizegenetics.plugindef.AbstractPlugin - 0
java.lang.ArrayIndexOutOfBoundsException: 0
        at org.ejml.data.D1Matrix64F.get(Unknown Source)
        at org.ejml.alg.dense.mult.MatrixVectorMult.mult(Unknown Source)
        at org.ejml.ops.CommonOps.mult(Unknown Source)
        at net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix.mult(EJMLDoubleMatrix.java:290)
        at net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix.testMarkerUsingP3D(CompressedMLMusingDoubleMatrix.java:824)
        at net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix.solve(CompressedMLMusingDoubleMatrix.java:440)
        at net.maizegenetics.analysis.association.WeightedMLMPlugin.processData(WeightedMLMPlugin.java:251)
        at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
        at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1538)
        at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1554)
        at net.maizegenetics.analysis.data.CombineDataSetsPlugin.performFunction(CombineDataSetsPlugin.java:65)
        at net.maizegenetics.analysis.data.CombineDataSetsPlugin.dataSetReturned(CombineDataSetsPlugin.java:126)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
        at net.maizegenetics.analysis.data.CombineDataSetsPlugin.performFunction(CombineDataSetsPlugin.java:65)
        at net.maizegenetics.analysis.data.CombineDataSetsPlugin.dataSetReturned(CombineDataSetsPlugin.java:126)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

[Peter Bradbury]

Was the data filtered for coverage and minor allele frequency? Is it possible that there are a few sites that are monomorphic or have all missing data after the intersect join?

Peter

[Ginnie M]

I just double checked. There do not seem to be any monomorphic sites nor sites with no data at all. The data were filtered such that the minor allele frequency is ~0.0005 (at least one individual w/ a minor allele). Raising the threshold to at least 2 individuals w/ a minor allele returns the same error.

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