MLM error

[Fernando]

Hello, I have a problem when I am trying to run MLM analysis in maize to do GWAS in Tassel 4. I've uploaded the following files in Tassel: Phenotype (traits), Genotype (imputed GBS SNPs), K matrix and population structure (I have excluded one of the three subpopulations e.g. Q3); so, I combined the files (genotype + filtered structure+ trait) by intersecting taxa (U join); subsequently I have selected the combined data set and the kinship matrix and I made click on the MLM tab. I chose “optimum level” and “P3D” option and I run it, I give an Output base file name, After two minutes approximately an error window projected. What could be my problem?

Thank you.

Pd. My machine has 8 gb of ram and I've increased the heap size until 6 gb and a screenshot is attached.

[Peter Bradbury]

To get an informative error message enable the Java console. In Windows, go to the Control Panel, double click the Java icon, then click "show console" on the Advanced tab. After that, when you run Tassel (or any other java program) the console will open and display messages generated as the program runs.

Peter

[Fernando]

I attached the informative error message in the Java console; I don't know exactly what may be the problem. Thank you Peter.

Fernando

[Peter Bradbury]

It is difficult to tell exactly what the problem is. There are two
separate errors. The first is that java failed to open a file for
output because access was denied. Possibly it was the name of an
existing file that was open in another application. The second was
seems to be because Tassel thinks a marker has a negative degrees of
freedom, which does not make sense. I don't know if that is an
indirect result of the first error or a problem with the input
genotypes.

Peter

>  MLM error.jpg
> 355KViewDownload

[Fernando]

I’m trying to do the analysis with Tassel 3 in pipeline, but I also have problems, I am using the following code:

.\run_pipeline.bat –Xms512m –Xmx6g –fork1 –a Chr10.txt –fork2 –t 267Blups_CB_13.txt –fork3 –r Population_structure_5kSNP.txt –excludeLast –fork4 –k Kinship_matrix_5kSNP.txt –combine5 –input1 –input2 –input3 –intersect –combine6 –input5 –input4 –mlm –mlmVarCompEst P3D –mlmCompressionLevel Optimum –export mlm_outputs –runfork1 –runfork2 –runfork3 –runfork4

The error message is the following:

.\sTASSEL.jar;.\lib\axiom-api-1.2.4.jar;.\lib\axiom-impl-1.2.4.jar;.\lib\axis2-k

ernel-1.2.jar;.\lib\batik-awt-util.jar;.\lib\batik-css.jar;.\lib\batik-dom.jar;.

\lib\batik-ext.jar;.\lib\batik-gui-util.jar;.\lib\batik-gvt.jar;.\lib\batik-pars

er.jar;.\lib\batik-svg-dom.jar;.\lib\batik-svggen.jar;.\lib\batik-util.jar;.\lib

\batik-xml.jar;.\lib\biojava3-alignment-3.0.jar;.\lib\biojava3-core-3.0.jar;.\li

b\biojava3-phylo-3.0.jar;.\lib\cisd-jhdf5-batteries_included_lin_win_mac.jar;.\l

ib\colt.jar;.\lib\commons-codec-1.3.jar;.\lib\commons-collections-3.1.jar;.\lib\

commons-configuration-1.2.jar;.\lib\commons-dbcp-1.2.1.jar;.\lib\commons-discove

ry.jar;.\lib\commons-httpclient-3.0.1.jar;.\lib\commons-lang-2.1.jar;.\lib\commo

ns-logging-1.1.jar;.\lib\commons-math-2.2.jar;.\lib\commons-pool-1.3.jar;.\lib\c

rimson-parser.jar;.\lib\ejml-0.13.jar;.\lib\forester.jar;.\lib\gdpc.jar;.\lib\ge

ronimo-spec-activation-1.0.2-rc4.jar;.\lib\jcommon-1.0.6.jar;.\lib\jfreechart-1.

0.3.jar;.\lib\jgrapht-0.5.3.jar;.\lib\jung-1.7.5.jar;.\lib\junit-4.1.jar;.\lib\L

iuExt.jar;.\lib\log4j-1.2.13.jar;.\lib\lzma-4.63-jio-0.93.jar;.\lib\mail-1.4.jar

;.\lib\mysql-connector-java-3.1.13-bin.jar;.\lib\poi-3.0.1-FINAL-20070705.jar;.\

lib\ssj.jar;.\lib\wsdl4j-1.6.2.jar;.\lib\xercesImpl.jar;.\lib\xml.jar;.\lib\xmlP

arserAPIs.jar;.\lib\XmlSchema-1.3.1.jar

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 3.0.146

 Date: January 10, 2013

java.lang.IllegalArgumentException: TasselPipeline: parseArgs: expecting argumen

t beginning with dash: ûXms512m

        at net.maizegenetics.pipeline.TasselPipeline.parseArgs(TasselPipeline.ja

va:180)

        at net.maizegenetics.pipeline.TasselPipeline.<init>(TasselPipeline.java:

121)

        at net.maizegenetics.pipeline.TasselPipeline.main(TasselPipeline.java:16

1)

Regards

[Terry Casstevens]

Hi,

These flags don't work with the .bat...
–Xms512m –Xmx6g

You need to edit that script directly. If you can provide me with the
.bat code to do the same as the perl version, I'd be happy to add it
to the official build.

Cheers,

Terry

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[Fernando]

[Fernando]

Hi Terry,

 

Actually I’ve only modified the head size available to Tassel Pipeline on the run_pipeline.bat file. So, the .bat code is.

 

@echo off

 

set TOP=.

set LIB_JARS=%TOP%\lib

 

set CP=%TOP%\sTASSEL.jar

for %%i in (%LIB_JARS%\*.jar) do call "%TOP%\cp.bat" %%i

echo %CP%

 

java -classpath "%CP%" -Xms512m –Xmx6g

net.maizegenetics.pipeline.TasselPipeline %*

 

You mean that code?

 

Fernando

[Claudia Perea]

Hello,

I'm having the same problem that you were discussing at the beggining of the post, using Tassel4, where an error window is displayed after uploading my two data sets and trying to  run  MLM. Apparently is a  common problem, as other people in the forum have reported it too, but I haven't find the answer on how to solve it for what I've read.  So I wanted to know, were you able to finally fixed it using Tassel 3 in pipeline? It would be usefull to know if that is the best way to run my data before start working in how to run the pipeline.
Appreciate any suggestions.

Claudia

[AAWT]

Hi all, I also got the same problem while trying MLM in TASSEL 4, and java console have the following error messages , please help me to solve this problem,

java.lang.NegativeArraySizeException
        at org.ejml.data.DenseMatrix64F.<init>(Unknown Source)
        at net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix.<init>(EJMLDo
ubleMatrix.java:39)
        at net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.make(Doubl
eMatrixFactory.java:39)
        at net.maizegenetics.stats.MLM.CompressedMLMusingDoubleMatrix.testMarker
UsingP3D(CompressedMLMusingDoubleMatrix.java:780)
        at net.maizegenetics.stats.MLM.CompressedMLMusingDoubleMatrix.solve(Comp
ressedMLMusingDoubleMatrix.java:335)
        at net.maizegenetics.baseplugins.MLMPlugin.performFunction(MLMPlugin.jav
a:137)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPl
ugin.java:201)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPlugin
Listener.java:29)

Thanks

AAWT

[Peter Bradbury]

I have been traveling so have not had time to look at this problem until today. I found the recently introduced change that was causing the error and fixed it. The fix will be included in the next build (probably later today). Thanks to you and other for calling this to our attention.

Peter

On Wednesday, February 13, 2013 7:16:44 PM UTC-5, Fernando wrote:

[Terry Casstevens]

The new build is now available.

Cheers,

Terry

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