Tassel 3.0 Memory Problems

[KJK]

I've tried to run the GBS pipeline on Tassel 4.0 and was successful up to a point. I did not have any issues until a SNP plugin.

I am trying to run Tassel 3.0 and can't even get started for unknown reasons.

I am running Ubuntu 12.04 and have 8 gigabytese of ram available. I have tried every variation of minimum and maximum memory usgae using both the command line (see below) and manually editing the run_pipeline.pl file.

This is the exact code I use:

perl run_pipeline.pl -Xmx6g -fork1 -FastqToTagCountPlugin -i fastq -k keys.txt -e apeki -o tagCounts -endPlugin -runfork1

And this is the errors it spits out:

Memory Settings: -Xms512m -Xmx6g
Tassel Pipeline Arguments: -fork1 -FastqToTagCountPlugin -i fastq -k keys.txt -e apeki -o tagCounts -endPlugin -runfork1
Invalid maximum heap size: -Xmx6g
The specified size exceeds the maximum representable size.
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.


I applaud any advice.

[Jeff Glaubitz]

Sounds like you are on a 32 bit machine that can’t exceed 4g, or some maximum setting regarding the Java Virtual Machine.  But that doesn’t make sense if Tassel4 could run with these memory settings.

 

Any ideas Terry?

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[Terry Casstevens]

There is probably a mismatch between your Java and OS. They Should
both either be 32 bit or 64 bit. Type java -version to check java to
see if it's the same as your OS.

Cheers,

Terry

On Mon, Feb 18, 2013 at 11:45 AM, Jeff Glaubitz <jcg...@cornell.edu> wrote:
> Sounds like you are on a 32 bit machine that can’t exceed 4g, or some
> maximum setting regarding the Java Virtual Machine. But that doesn’t make
> sense if Tassel4 could run with these memory settings.
>
>
>
> Any ideas Terry?
>
>
>
>
>
> From: tas...@googlegroups.com [mailto:tas...@googlegroups.com] On Behalf Of
> KJK
> Sent: Monday, February 18, 2013 11:39 AM
> To: tas...@googlegroups.com
> Subject: [TASSEL-Group] Tassel 3.0 Memory Problems
>
>
>

[Sandip Kale]

Hi Terry,

I am also getting the same error on Windows.
I have Windows 8 and cmd looks like 32 bit : C:\Windows\system32

G:\Softwares\tassel4.0_standalone>java -Xms256M -Xmx 7000
Invalid maximum heap size: -Xmx

Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

What Should I do in this case? Also, Once I increase the memory can I use the GUI version?

Thank you in advance

[Terry Casstevens]

Please edit start_tassel.bat to increase heap with something like (no
space after -Xmx)

-Xmx5g

And run start_tassel.bat to start GUI.

> https://groups.google.com/d/msgid/tassel/ababcc77-81ad-42f3-9b5d-21cdce046b72%40googlegroups.com.

[Sandip Kale]

Hi terry,

I make the changes suggested, however, I am still getting the error:

G:\Softwares\tassel4.0_standalone>start_tassel.bat
.\sTASSEL.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-1.5.jar;.\lib\commons-math-2.2.jar;.\lib\ejml-0.
13.jar;.\lib\forester.jar;.\lib\geronimo-spec-activation-1.0.2-rc4.jar;.\lib\ite
xtpdf-5.1.0.jar;.\lib\jcommon-1.0.6.jar;.\lib\jfreechart-1.0.3.jar;.\lib\junit-4
.1.jar;.\lib\LiuExt.jar;.\lib\log4j-1.2.13.jar;.\lib\mail-1.4.jar;.\lib\poi-3.0.
1-FINAL-20070705.jar;.\lib\xercesImpl.jar;.\lib\xml.jar;.\lib\xmlParserAPIs.jar
Invalid maximum heap size: -Xmx4g

The specified size exceeds the maximum representable size.
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

Please help

[Terry Casstevens]

How much RAM does your system have? Try a lower number 3g? 2g?

> https://groups.google.com/d/msgid/tassel/14ee1820-c1dc-4f3a-a2cb-165c09bfb059%40googlegroups.com.