First guess is that perhaps the system is still defaulting to using java 1.6 and not 1.7. What happens if you run “java -version” as the Galaxy system user? Perhaps try a reboot of the vm as well to make sure that the Galaxy app is running with java 1.7.
Also, is this a custom vm? If it using running things on different cluster nodes, you’ll need to make sure the java version on those nodes are 1.7 as well.
Thanks,
Dan
On Oct 10, 2014, at 3:04 PM, Iry Witham Iry.Witham@jax.org wrote:
Hi Team,
I am sorry to be a pest, but I am under-the-gun to get this resolved. I have followed the instructions for installing GATK2 on my cloud VM. After doing that I discovered that the version of java running on the VM was v1.6.x and GATK2 required v1.7.0x. I removed version 6 and installed version 7, uninstalled GATK2 and reinstalled it and reset all of the settings that may have reverted with the uninstalls/reinstalls. Now when I run Unified Genotyper I get the following error:
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:643) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:277) at java.net.URLClassLoader.access$000(URLClassLoader.java:73) at java.net.URLClassLoader$1.run(URLClassLoader.java:212) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:323) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:268) Could not find the main class: org.broadinstitute.gatk.engine.CommandLineGATK. Program will exit.
Researching this I found a post at http://gatkforums.broadinstitute.org/discussion/3378/gatk2-error-when-i-test... that refers to upgrading java as the solution. However, that did not fix the issue. In addition I copied the jar file to a temp directory and unzipped it to examine the MANAFEST.MF file for versioning issues. This is what I found:
Manifest-Version: 1.0 Build-Jdk: 1.7.0_51 Built-By: gsa-engineering Created-By: Apache Maven Main-Class: org.broadinstitute.gatk.engine.CommandLineGATK Archiver-Version: Plexus Archiver
This tells me that there is something else causing the problem. Does anyone have an idea where to look now?Regards,Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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