Hi Dan,

I had suspected that, but when I run java –version I get the following:

java version "1.7.0_65"
OpenJDK Runtime Environment (IcedTea 2.5.1) (7u65-2.5.1-4ubuntu1~0.12.04.2)
OpenJDK 64-Bit Server VM (build 24.65-b04, mixed mode)

I have rebooted the VM and nothing has changed.  The VM is built on AWS cloud 
and is using the latest galaxy ami:


  1.  AMI: ami-a7dbf6ce
  2.  Name: Galaxy CloudMan<https://wiki.galaxyproject.org/CloudMan> 2.3

The only difference is that I needed to upgrade the java version for GATK2 and 
snpEff.  I currently have just a single node running so there is no issue with 
the wrong java version running on additional nodes.

Thanks,
Iry

From: Daniel Blankenberg <d...@bx.psu.edu<mailto:d...@bx.psu.edu>>
Date: Friday, October 10, 2014 3:16 PM
To: Iry Witham <iry.wit...@jax.org<mailto:iry.wit...@jax.org>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: Re: [galaxy-dev] GATK2 java version related issues

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.wit...@jax.org<mailto:iry.wit...@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-tested-it-after-installing
 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
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