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Problem with Scala running Queue.jar

Hi,

I'm new to GATK, and I've been trying to run the Installation Testing instructions here. I've gotten stuck at the Queue.jar example. Here's what I get (running GATK compiled from the Git repo, Java version

$ java -version
java version "1.7.0_03"
OpenJDK Runtime Environment (IcedTea7 2.1.3) (7u3-2.1.3-1)
OpenJDK 64-Bit Server VM (build 22.0-b10, mixed mode)
[email protected] gatk_test $ java -Djava.io.tmpdir=tmp -jar ~/local/gatk/dist/Queue.jar -S ExampleCountReads.scala -R /home/zack/data/gatk_resource_bundle/1.5/exampleFASTA/exampleFASTA.fasta -I /home/zack/data/gatk_resource_bundle/1.5/exampleFASTA/exampleBAM.bam
INFO  18:59:45,057 QScriptManager - Compiling 1 QScript 
ERROR 18:59:45,060 QScriptManager - IO error while decoding ExampleCountReads.scala with UTF-8
Please try specifying another one using the -encoding option 
ERROR 18:59:45,061 QScriptManager - one error found 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
org.broadinstitute.sting.queue.QException: Compile of ExampleCountReads.scala failed with 1 error
        at org.broadinstitute.sting.queue.QScriptManager.loadScripts(QScriptManager.scala:46)
        at org.broadinstitute.sting.queue.QCommandLine.org$broadinstitute$sting$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:95)
        at org.broadinstitute.sting.queue.QCommandLine.getArgumentSources(QCommandLine.scala:191)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:197)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
        at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
        at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.2-16-g2cc9ef8):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Compile of ExampleCountReads.scala failed with 1 error
##### ERROR ------------------------------------------------------------------------------------------
INFO  18:59:45,186 QCommandLine - Shutting down jobs. Please wait... 

I've tried: Using Sun Java 1.6 (I get "Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/commandline/CommandLineProgram : Unsupported major.minor version 51.0"), compiling with Sun Java 1.6 instead of OpenJDK 1.7, reinstalling Scala.

Thanks for any help.

Best Answer

Answers

  • nicholsznicholsz Member

    Ah, that did it. Thanks very much.

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