I am running the following command to test my scala using GATK-2.3.5
> java -Xmx4g -Djava.io.tmpdir=tmp -jar /Queue-2.3-5-g49ed93c/Queue.jar -S Queue-2.3-5-g49ed93c/ExampleCountReads.scala -R /GATK-2.3-5-g49ed93c/resources/exampleFASTA.fasta -I /GATK-2.3-5-g49ed93c/resources/exampleBAM.bam
and I am getting this error
> INFO 13:42:55,166 QScriptManager - Compiling 1 QScript
> ERROR 13:42:55,348 QScriptManager - ExampleCountReads.scala:39: in XML literal: '=' expected instead of 'G'
> ERROR 13:42:55,356 QScriptManager - // java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help
> ERROR 13:42:55,356 QScriptManager - ^
> ERROR 13:42:55,357 QScriptManager - ExampleCountReads.scala:39: in XML literal: ' or " delimited attribute value or '{' scala-expr '}' expected
> ERROR 13:42:55,358 QScriptManager - // java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help
> ERROR 13:42:55,358 QScriptManager - ^
> ERROR 13:42:55,358 QScriptManager - ExampleCountReads.scala:39: in XML literal: whitespace expected
> ERROR 13:42:55,359 QScriptManager - // java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help
> ERROR 13:42:55,360 QScriptManager - ^
> ERROR 13:42:55,360 QScriptManager - ExampleCountReads.scala:39: in XML literal: '=' expected instead of '>'
> ERROR 13:42:55,361 QScriptManager - // java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help
> ERROR 13:42:55,362 QScriptManager - ^
> ERROR 13:42:55,362 QScriptManager - ExampleCountReads.scala:39: in XML literal: ' or " delimited attribute value or '{' scala-expr '}' expected
> ERROR 13:42:55,363 QScriptManager - // java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help
> ERROR 13:42:55,365 QScriptManager - ^
> ERROR 13:42:55,366 QScriptManager - ExampleCountReads.scala:39: in XML literal: whitespace expected
> ERROR 13:42:55,367 QScriptManager - // java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help
> ERROR 13:42:55,367 QScriptManager - ^
> ERROR 13:42:55,367 QScriptManager - ExampleCountReads.scala:39: in XML literal: '>' expected instead of ' '
> ERROR 13:42:55,369 QScriptManager - // java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help
> ERROR 13:42:55,369 QScriptManager - ^
> ERROR 13:42:55,369 QScriptManager - ExampleCountReads.scala:67: in XML literal: in XML content, please use '}}' to express '}'
> ERROR 13:42:55,369 QScriptManager - }
> ERROR 13:42:55,369 QScriptManager - ^
> ERROR 13:42:55,370 QScriptManager - ExampleCountReads.scala:39: I encountered a '}' where I didn't expect one, maybe this tag isn't closed <WalkerName>
> ERROR 13:42:55,371 QScriptManager - // java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help
> ERROR 13:42:55,371 QScriptManager - ^
> ERROR 13:42:55,371 QScriptManager - ExampleCountReads.scala:68: '}' expected but eof found.
> ERROR 13:42:55,371 QScriptManager - }
> ERROR 13:42:55,372 QScriptManager - ^
> ERROR 13:42:55,390 QScriptManager - 10 errors found
> ##### ERROR ------------------------------------------------------------------------------------------
> ##### ERROR stack trace
> org.broadinstitute.sting.queue.QException: Compile of /medpop/mpg-psrl/Parabase/Tools/Queue-2.3-5-g49ed93c/ExampleCountReads.scala failed with 10 errors
> at org.broadinstitute.sting.queue.QScriptManager.loadScripts(QScriptManager.scala:46)
> at org.broadinstitute.sting.queue.QCommandLine.org$broadinstitute$sting$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:94)
> at org.broadinstitute.sting.queue.QCommandLine.getArgumentSources(QCommandLine.scala:225)
> 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:61)
> at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
> ##### ERROR ------------------------------------------------------------------------------------------
> ##### ERROR A GATK RUNTIME ERROR has occurred (version 2.3-5-g49ed93c):
> ##### 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 /medpop/mpg-psrl/Parabase/Tools/Queue-2.3-5-g49ed93c/ExampleCountReads.scala failed with 10 errors
> ##### ERROR ------------------------------------------------------------------------------------------
> INFO 13:42:55,487 QCommandLine - Shutting down jobs. Please wait...
> 13.462u 1.029s 0:10.41 139.0% 0+0k 0+0io 1pf+0w
>
I am sure java, gatk and queue are installed properly and the files exist in the relevant directory. Thank you,