TASSEL PCA not working

[Jen]

Hello,

I recently updated my TASSEL standalone and have found the PCA feature no longer works -- a small dataset causes the program to crash. Interestingly, this used to work just fine on an earlier version of TASSEL 4.0. Not sure which version I was running before, but it is earlier than V4.0.23, because I tried switching back to this version via git and had the same error. Is it possible to update back to an older version? Or, even better, can the implementation of the PCA feature be restored?

Thanks,

Jen

[Terry Casstevens]

Hi Jen,

Can you be more specific what steps you are taking? And also provide
a sample file? What error messages are you getting?

Yes, you can use Git retrieve earlier versions. See this document:
http://www.maizegenetics.net/tassel/docs/UpdatingTasselStandaloneUsingGit.pdf.
Please let me know if you find the version where it stopped working,
so that I can more easily diagnose the problem.

Cheers,

Terry

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[Jen]

Hi Terry,

Actually, I just solved this problem. I was looking at the bug-tracking on sourceforge, and found the notice that PCA in TASSEL4 hangs when there are monomorphic markers in the dataset. I removed the monomorphic markers, and the problem was solved. 

Specifically, I was doing a simple file load, followed by collapse non-major alleles, followed by basic impute, followed by PCA. 

Thanks!

Jen

[AAWT]

Hi,
I am running TASSEL4 for PCA, after removing minor SNPs, it is runing since one week and messages in java console are :

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionLi
stener: node type: class net.maizegenetics.pal.alignment.BitNucleotideAlignment
[Thread-4] INFO net.maizegenetics.baseplugins.FilterAlignmentPlugin - Resulting
Number Sites: 4502
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionLi
stener: node type: class net.maizegenetics.pal.alignment.FilterAlignment
[Thread-5] INFO net.maizegenetics.pal.alignment.BitAlignment - optimizeForSites:
 Already Optimized for Sites.
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionLi
stener: node type: class net.maizegenetics.pal.popgen.LinkageDisequilibrium
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionLi
stener: Table Report Size: 172239767
java.lang.ArrayIndexOutOfBoundsException: 4502
        at net.maizegenetics.pal.alignment.FilterAlignment.translateSite(FilterA
lignment.java:445)
        at net.maizegenetics.pal.alignment.FilterAlignment.getLocusName(FilterAl
ignment.java:826)
        at net.maizegenetics.pal.gui.LinkageDisequilibriumComponent.<init>(Linka
geDisequilibriumComponent.java:86)
        at net.maizegenetics.baseplugins.LinkageDiseqDisplayDialog.<init>(Linkag
eDiseqDisplayPlugin.java:227)
        at net.maizegenetics.baseplugins.LinkageDiseqDisplayPlugin.performFuncti
on(LinkageDiseqDisplayPlugin.java:60)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPl
ugin.java:201)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPlugin
Listener.java:29)
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionLi
stener: node type: class net.maizegenetics.pal.alignment.FilterAlignment
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionLi
stener: node type: class net.maizegenetics.pal.alignment.SimplePhenotype
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionLi
stener: Table Report Size: 2319045
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionLi
stener: node type: class net.maizegenetics.pal.alignment.SimplePhenotype
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionLi
stener: Table Report Size: 2287524
Doing singularValueDecomposition..., please wait.
,
please guide me how to solve problem

Best Regards