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Executing TASSEL

This page describes how to launch TASSEL, adjust the Java heap size for the GUI and command line, and troubleshoot common startup errors. For the full command-line flag reference, see the Pipeline Reference and the GBSv2 Pipeline.

Change Heap Size (GUI)

TASSEL runs on the Java Virtual Machine, which reserves a fixed range of memory called the heap. Increase the maximum heap (-Xmx) if you run out of memory on large datasets.

macOS

  1. In the Applications folder, double-click TASSEL 5.
  2. Right-click the TASSEL 5 application and choose Show Package Contents.
  3. Open the Contents folder.
  4. Edit the file vmoptions.txt.
  5. Change -Xms (minimum heap, e.g. -Xms512m) and -Xmx (maximum heap, e.g. -Xmx5g) as appropriate.

Windows

  1. Go to the TASSEL installation directory (default: C:\Program Files\TASSEL5).
  2. Edit the file Tassel 5.vmoptions.
  3. Change -Xms (minimum heap, e.g. -Xms512m) and -Xmx (maximum heap, e.g. -Xmx5g) as appropriate.

Note

If User Account Control (UAC) is enabled, start your text editor with Run as administrator before editing Tassel 5.vmoptions.

Command Line (macOS / Linux / Windows Bash)

Add the TASSEL directory to your PATH so you can run the scripts from any location, for example in .bash_profile:

PATH=$PATH:/analysis_tools/tassel5.0_standalone

Then use these commands:

./start_tassel.pl -Xmx4g   # Start the GUI with a 4 GB max heap size
./run_pipeline.pl -Xmx5g   # Run the command line with a 5 GB max heap size

Command Line (Windows)

start_tassel.bat   :: Start the GUI
run_pipeline.bat   :: Run the command line

Note

To increase the heap size, edit the .bat file you are using and change the -Xmx parameter.

Troubleshooting

Could not create the Java Virtual Machine

If you get an error message containing Error: Could not create the Java Virtual Machine, The specified size exceeds the maximum representable size, or Could not reserve enough space for 2097152KB object heap, you most likely have a mismatch between your Java installation and operating system: one is 32-bit and the other is 64-bit.

Run java -version to check whether your Java matches your operating system. Note that there may be multiple Java installations on your machine, and your web browser may use a different one than your command line. Run java -d64 -version to see if your installation supports 64-bit.

See the Oracle HotSpot heap FAQ for details.

Invalid maximum heap size

Invalid maximum heap size: -Xmx4g
The specified size exceeds the maximum representable size.
Error: Could not create the Java Virtual Machine.

This may be due to a limit on the maximum heap, which is system dependent. Try reducing the -Xmx setting.

UnsupportedClassVersionError

Exception in thread "main" java.lang.UnsupportedClassVersionError:
net/maizegenetics/pipeline/TasselPipeline : Unsupported major.minor version 51.0

You need a higher version of Java. TASSEL 5 requires Java 1.8.

Could not find or load main class

If you get Error: Could not find or load main class net.maizegenetics.tassel.TASSELMainApp while running start_tassel.pl or run_pipeline.pl in the Bash shell on Windows, change the following line to use a ; instead of a :.

my $CP = join(":", @fl);

macOS Gatekeeper

TASSEL does not have an Apple signature, so you may need to adjust Gatekeeper to install the program. See Apple's instructions.