GATK2 java version related issues

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GATK2 java version related issues

Iry Witham
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

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.


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Re: GATK2 java version related issues

Daniel Blankenberg
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 <[hidden email]> 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
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/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
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Re: GATK2 java version related issues

Iry Witham
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 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 <[hidden email]>
Date: Friday, October 10, 2014 3:16 PM
To: Iry Witham <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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
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/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/