Java version with QUEUE.
Posted in Ask the team | Last updated on 2013-10-08 05:14:30


Comments (3)

Hi team,
I have Java 1.6 installed in my system. I know that GATK works now with Java 1.7, but I work in a shared system and I can not change the default java version so I downloaded Java 1.7 and I work asigning the java version at the call:

If I run:
/jre1.7.0/bin/java -Djava.io.tmpdir=tmp -jar Queue.jar --help
works fine, but if I try:
/jre1.7.0/bin/java -Djava.io.tmpdir=tmp -jar Queue.jar -S myScala.file ....
I get the following error:

DEBUG 13:42:50,953 FunctionEdge - Starting: /Qscripts > 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/Qscripts/tmp' '-cp' 'Queue.jar' 'org.broadinstitute.sting.gatk.CommandLineGATK' '-T' 'HaplotypeCaller' '-I' '/resources/exampleBAM.bam' '-R' '/resources/exampleFASTA.fasta' '-nct' '1' '-o' '/raw1.vcf' '-hets' '0.005'
INFO 13:42:50,954 FunctionEdge - Output written to /raw1.vcf.out DEBUG 13:42:50,954 IOUtils - Deleted /raw1.vcf.out Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/gatk/CommandLineGATK : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631) at java.lang.ClassLoader.defineClass(ClassLoader.java:615) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141) at java.net.URLClassLoader.defineClass(URLClassLoader.java:283) at java.net.URLClassLoader.access$000(URLClassLoader.java:58) at java.net.URLClassLoader$1.run(URLClassLoader.java:197) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:190) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:247) Could not find the main class: org.broadinstitute.sting.gatk.CommandLineGATK. Program will exit.

Seems like if HaplotypeCaller call java again and use the default java in the system, that is Java 1.6

Can I change the "java" version parameter?

Thanks in advance,


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