Fail to generate Manhattan plot

[Cecilia]

Hi,

 

I'm using TASSEL4.0 Standalone version and followed instructions on "Demonstration of TASSEL". The hapmap and traits files were joined, GLM model was generated without any difficulty. But when I tried to create Manhattan Plot, I got "Unable to create Manhattan plot java.lang.OutofMemoryError: Java heap space". QQ plot was created without problem.

 

Clicked on 'Show Memory' showed Current Heap Size of 10,201.16 KB. The command I started TASSEL was "java -Xms512M -Xmx1200M -jar sTASSEL.jar". The computer I'm using is Windows 7 with 8GB installed RAM.

 

The dataset is small, with only 3606 SNP sites and 48 taxa.

 

Can anyone help please? Thanks!

[Terry Casstevens]

Hi Cecilla,

I agree, it should handle that small data set easily. I generally
recommend using start_tassel.bat or start_tassel.pl. But I tried your
command exactly and went through the task you indicate. It worked for
me. Can you find the logging message on the command line showing the
max heap that looks like this?

[main] INFO net.maizegenetics.tassel.TASSELMainFrame - Max Available
Memory Reported by JVM: 1185 MB

Cheers,

Terry

> --
> You received this message because you are subscribed to the Google Groups
> "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to tassel+un...@googlegroups.com.
> To post to this group, send email to tas...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/tassel/5e9195a2-5110-4748-aa39-0dd630f718f6%40googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>

[Cecilia]

Hi Terry,

 

I re-ran TASSEL4.0 with different data set, but always failed at generating manhattan plots.

 

The max heap shown was:

 

[main] INFO net.maizegenetics.tassel.TASSELMainFrame - Tassel Version: 4.1.32  Date: May 23, 2013

[main] INFO net.maizegenetics.tassel.TASSELMainFrame - Max Available Memory Reported by JVM: 1365 MB

 

The logs looked ok until I tried to generate manhattan plots:

 

========

Kinship was built from markers

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.pal.alignment.MarkerPhenotype

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - This is not serializable.

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: Table Report Size: 144

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.pal.report.SimpleTableReport

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: Table Report Size: 86256

java.lang.OutOfMemoryError: Java heap space at net.maizegenetics.baseplugins.chart.TableReportManhattanDataset.setTa

bleReport(TableReportManhattanDataset.java:242) at net.maizegenetics.baseplugins.chart.TableReportManhattanDataset.<init

>(TableReportManhattanDataset.java:48)

        at net.maizegenetics.baseplugins.chart.XYScatterMultipleYPanel.<init>(XY ScatterMultipleYPanel.java:39)

        at net.maizegenetics.baseplugins.ManhattanDisplayPluginDialog.<init>(ManhattanDisplayPlugin.java:163)

        at net.maizegenetics.baseplugins.ManhattanDisplayPlugin.performFunction(

ManhattanDisplayPlugin.java:62)

        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)

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

=========

The possible reasons that I can think of include:

*  in-correct format of my input files (hapmap or traits), but the data loading and joining steps didn't complain

*  the number of scaffolds is too many and TASSEL failed to handle it properly.

 

I attached the traits and hapmap files with this email. Do you mind testing it on your machine and see if the problem repeat at your side?

 

The steps that I carried out are:

* start_tassel.bat

* load hapmap file

* load traits file

* Intersect-join hapmap and traits datasets

* Select hapmap and create Kinship

* Select the merged file (hapmap+traits) and the kinship, then Analysis-> MLM

* Select MLM statistics result, then Results->Manhattan

 

 

Thank you very much!

 

Cheers,
Cecilia

[Nicholi Pitra]

hello all,

Did the  "This is not serializable." problem ever get resolved?

 I have found that it is quite common wile running MLM and have found several ways to trouble shoot it but now i am seeing it again and can not seem to get around it. Do we know what it means exactly?