Dominant data analysis using Tassel 5 and kinship analysis

[neha roy]

Hello,

I m trying to analyse dominant marker data using Tassel 5, but i m unable to calculate the kinship. I have updated the program to it's latest version (5.2.29), but it always gives an error of "null". Can anyone kindly send me a tutorial for using tassel for dominant data.

Thank you

[Terry Casstevens]

Please read this how to report your problem
https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf



Tassel User Group...
http://groups.google.com/group/tassel

Tassel Web Site..
http://www.maizegenetics.net/tassel

Tassel 5 User Manual...
https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual

Tassel Wiki...
https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Home

Tassel 5 Change History...
http://tassel.bitbucket.org/docs/Tassel5ChangeHistory.html



Best,

Terry

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[neha roy]

[Thread-7] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.29  Date: August 4, 2016

[Thread-7] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 1801 MB

[Thread-7] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_40

[Thread-7] INFO net.maizegenetics.tassel.TasselLogging - OS: Windows 7

[Thread-7] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 4

[Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.tassel.TasselLogging: time: Aug 30, 2016 9:50:38

[Thread-9] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.tassel.TasselLogging: time: Aug 30, 2016 9:53:42

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.dna.snp.CoreGenotypeTable

[Thread-10] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.distance.KinshipPlugin: time: Aug 30, 2016 9:53:52

[Thread-10] INFO net.maizegenetics.plugindef.AbstractPlugin - 

KinshipPlugin Parameters

method: Normalized_IBS

maxAlleles: 6

algorithmVariation: Observed_Allele_Freq

[Thread-10] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null

java.lang.NullPointerException

at net.maizegenetics.dna.snp.CoreGenotypeTable.genotypeAllTaxa(CoreGenotypeTable.java:105)

at net.maizegenetics.analysis.distance.GCTADistanceMatrix$GCTASiteSpliterator.getBlockOfSites(GCTADistanceMatrix.java:520)

at net.maizegenetics.analysis.distance.GCTADistanceMatrix$GCTASiteSpliterator.forEachRemaining(GCTADistanceMatrix.java:430)

at java.util.stream.AbstractPipeline.copyInto(Unknown Source)

at java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)

at java.util.stream.ReduceOps$ReduceTask.doLeaf(Unknown Source)

at java.util.stream.ReduceOps$ReduceTask.doLeaf(Unknown Source)

at java.util.stream.AbstractTask.compute(Unknown Source)

at java.util.concurrent.CountedCompleter.exec(Unknown Source)

at java.util.concurrent.ForkJoinTask.doExec(Unknown Source)

at java.util.concurrent.ForkJoinTask.doInvoke(Unknown Source)

at java.util.concurrent.ForkJoinTask.invoke(Unknown Source)

at java.util.stream.ReduceOps$ReduceOp.evaluateParallel(Unknown Source)

at java.util.stream.AbstractPipeline.evaluate(Unknown Source)

at java.util.stream.ReferencePipeline.reduce(Unknown Source)

at net.maizegenetics.analysis.distance.GCTADistanceMatrix.computeGCTADistances(GCTADistanceMatrix.java:74)

at net.maizegenetics.analysis.distance.GCTADistanceMatrix.getInstance(GCTADistanceMatrix.java:62)

at net.maizegenetics.analysis.distance.KinshipPlugin.processData(KinshipPlugin.java:119)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

[Thread-11] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.distance.KinshipPlugin: time: Aug 30, 2016 9:54:3

[Thread-11] INFO net.maizegenetics.plugindef.AbstractPlugin - 

KinshipPlugin Parameters

method: Centered_IBS

maxAlleles: 6

algorithmVariation: Observed_Allele_Freq

[Thread-11] INFO net.maizegenetics.analysis.distance.EndelmanDistanceMatrix - EndelmanDistanceMatrix: estimated time: 0 minutes

[Thread-11] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null

java.lang.NullPointerException

at net.maizegenetics.dna.snp.CoreGenotypeTable.genotypeAllTaxa(CoreGenotypeTable.java:105)

at net.maizegenetics.analysis.distance.EndelmanDistanceMatrix$EndelmanSiteSpliterator.getBlockOfSites(EndelmanDistanceMatrix.java:531)

at net.maizegenetics.analysis.distance.EndelmanDistanceMatrix$EndelmanSiteSpliterator.forEachRemaining(EndelmanDistanceMatrix.java:441)

at java.util.stream.AbstractPipeline.copyInto(Unknown Source)

at java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)

at java.util.stream.ReduceOps$ReduceTask.doLeaf(Unknown Source)

at java.util.stream.ReduceOps$ReduceTask.doLeaf(Unknown Source)

at java.util.stream.AbstractTask.compute(Unknown Source)

at java.util.concurrent.CountedCompleter.exec(Unknown Source)

at java.util.concurrent.ForkJoinTask.doExec(Unknown Source)

at java.util.concurrent.ForkJoinTask.doInvoke(Unknown Source)

at java.util.concurrent.ForkJoinTask.invoke(Unknown Source)

at java.util.stream.ReduceOps$ReduceOp.evaluateParallel(Unknown Source)

at java.util.stream.AbstractPipeline.evaluate(Unknown Source)

at java.util.stream.ReferencePipeline.reduce(Unknown Source)

at net.maizegenetics.analysis.distance.EndelmanDistanceMatrix.computeEndelmanDistances(EndelmanDistanceMatrix.java:121)

at net.maizegenetics.analysis.distance.EndelmanDistanceMatrix.getInstance(EndelmanDistanceMatrix.java:97)

at net.maizegenetics.analysis.distance.KinshipPlugin.processData(KinshipPlugin.java:117)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

[Thread-12] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.distance.KinshipPlugin: time: Aug 30, 2016 9:54:12

[Thread-12] INFO net.maizegenetics.plugindef.AbstractPlugin - 

KinshipPlugin Parameters

method: Centered_IBS

maxAlleles: 2

algorithmVariation: Observed_Allele_Freq

[Thread-12] INFO net.maizegenetics.analysis.distance.EndelmanDistanceMatrix - EndelmanDistanceMatrix: estimated time: 0 minutes

[Thread-12] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null

java.lang.NullPointerException

at net.maizegenetics.dna.snp.CoreGenotypeTable.genotypeAllTaxa(CoreGenotypeTable.java:105)

at net.maizegenetics.analysis.distance.EndelmanDistanceMatrix$EndelmanSiteSpliterator.getBlockOfSites(EndelmanDistanceMatrix.java:531)

at net.maizegenetics.analysis.distance.EndelmanDistanceMatrix$EndelmanSiteSpliterator.forEachRemaining(EndelmanDistanceMatrix.java:441)

at java.util.stream.AbstractPipeline.copyInto(Unknown Source)

at java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)

at java.util.stream.ReduceOps$ReduceTask.doLeaf(Unknown Source)

at java.util.stream.ReduceOps$ReduceTask.doLeaf(Unknown Source)

at java.util.stream.AbstractTask.compute(Unknown Source)

at java.util.concurrent.CountedCompleter.exec(Unknown Source)

at java.util.concurrent.ForkJoinTask.doExec(Unknown Source)

at java.util.concurrent.ForkJoinTask.doInvoke(Unknown Source)

at java.util.concurrent.ForkJoinTask.invoke(Unknown Source)

at java.util.stream.ReduceOps$ReduceOp.evaluateParallel(Unknown Source)

at java.util.stream.AbstractPipeline.evaluate(Unknown Source)

at java.util.stream.ReferencePipeline.reduce(Unknown Source)

at net.maizegenetics.analysis.distance.EndelmanDistanceMatrix.computeEndelmanDistances(EndelmanDistanceMatrix.java:121)

at net.maizegenetics.analysis.distance.EndelmanDistanceMatrix.getInstance(EndelmanDistanceMatrix.java:97)

at net.maizegenetics.analysis.distance.KinshipPlugin.processData(KinshipPlugin.java:117)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

[Thread-13] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.tassel.TasselLogging: time: Aug 30, 2016 9:54:19

[Thread-13] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.tassel.TasselLogging: time: Aug 30, 2016 9:54:19

[Terry Casstevens]

What type of genotype file format are you using? This exception trace
indicates there are no genotype calls?

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[neha roy]

hello, 

Thank you for your response. I am using AFLP data, and when i am using the same in Tassel 3 it is working fine, but i m unable to get all the GLM tables, so I updated to Tassel 5 where it is showing this error while calculating kinship.

[Terry Casstevens]

Can you send me the file privately? Are a small example?

> https://groups.google.com/d/msgid/tassel/60a88d04-eaf1-4179-8f81-1a4a5d2deba4%40googlegroups.com.

[neha roy]

Yes, Please may i have you email id?

[Terry Casstevens]

tm...@cornell.edu

> https://groups.google.com/d/msgid/tassel/8ffe923f-6285-4aa9-b47b-53fdf5ec79cd%40googlegroups.com.

[Vincent Pinto]

Hello!!

I am pretty new to TASSEL.

I have AFLP data too and need to code them. What genotype table format to be used? How to code the numeric data? Using TASSEL 5.2.37. Please help me out.

Best,
Vincent