problem with Scala

naarkhoonaarkhoo Posts: 38Member
edited January 2013 in Ask the GATK team

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,

Post edited by Geraldine_VdAuwera on

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,962Administrator, GATK Developer admin

    Are you sure of the filepaths in your command line? It looks like you have them at the root of your filesystem.

    Geraldine Van der Auwera, PhD

  • naarkhoonaarkhoo Posts: 38Member

    I am sure, I have shorted the file-paths here; I double checked their existence using "tab" functionality in terminal. the scala error handling is not clear to me.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,962Administrator, GATK Developer admin

    That's strange, it looks like Queue is not parsing the script correctly. Did you try to modify the script at all?

    Can you tell me what operating system and version of java you are using?

    Geraldine Van der Auwera, PhD

  • naarkhoonaarkhoo Posts: 38Member

    here is the Java information : java version "1.6.0_0"
    OpenJDK Runtime Environment (IcedTea6 1.6) (rhel-1.11.b16.el5-x86_64)
    OpenJDK 64-Bit Server VM (build 14.0-b16, mixed mode)
    and I am using Linux node1387 2.6.18-194.8.1.el5 #1 x86_64 .... thank you

  • naarkhoonaarkhoo Posts: 38Member

    mmm, GATK by itself is fine. say I can run CountRead; Also I don't see any prerequisite issue with "java -jar Queue-2.3-5-g49ed93c/Queue.jar" command; do you still think it is prerequisite error ?! Thanks

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,962Administrator, GATK Developer admin

    You wouldn't get any warnings or error message specifically about the prerequisite because it's not something the program tests for at runtime; it's just that we don't test against that JDK and there are some reasons to believe that some functions will not work properly. GATK and Queue being two different programs, it is normal that one may not work where the other does. Unfortunately the developer of Queue is not available to comment on why Queue would be doing this. I have tested Queue-2.3-5 and I'm not seeing any issues parsing the supplied scala script. All I can recommend at this point is that you try with a different JDK or on a different machine. If you still have the same problem I can look into it further, but I cannot provide support as long as you are running with an unsupported configuration, sorry.

    Geraldine Van der Auwera, PhD

  • naarkhoonaarkhoo Posts: 38Member

    I had to ru "use .oracle-java-jdk-1.6.0-35-x86-64" here for loading the proper Java. Thanks

  • naarkhoonaarkhoo Posts: 38Member

    Still doesn't work, my java version is :
    java version "1.6.0_35"
    Java(TM) SE Runtime Environment (build 1.6.0_35-b10)
    Java HotSpot(TM) 64-Bit Server VM (build 20.10-b01, mixed mode)
    and the error is same.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,962Administrator, GATK Developer admin

    Hmm, so much for that. Are you using the binary from our website or did you compile from source?

    Geraldine Van der Auwera, PhD

  • naarkhoonaarkhoo Posts: 38Member

    I downloaded both Queue and GATK from your website; the exact version is 2.3-5-g49ed93c.

  • naarkhoonaarkhoo Posts: 38Member

    Can we flag the question as unanswered please !

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,962Administrator, GATK Developer admin

    I was working on diagnosing your problem, but if you're that impatient, sure I'll just drop it and flag it. It's not like I don't have anything else to work on.

    Geraldine Van der Auwera, PhD

  • naarkhoonaarkhoo Posts: 38Member

    no no ! sorry for miss-understanding ... I saw a couple of other post today and I thought might be you guys got overwhelmed with them ... anyway, I am sorry about that. Smile :-)

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,962Administrator, GATK Developer admin

    Ah, okay then, no worries :)

    We occasionally have people who think their problem is the most important in the world and get impatient if they don't get an answer immediately. We do have a lot on our plate and my temper flared up for a moment. All good now.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,962Administrator, GATK Developer admin

    Alright, I tested your install of GATK and Queue remotely, both are working fine. However it seems that your copy of the scala script must have got corrupted somehow, because when I run your command, with your install but my local copy of the script (same version), I get the same error you got. My recommendation is that you just re-download the Queue package; it should work with a fresh copy of the script. Good opportunity to upgrade to GATK 2.3-6 while you're at it.

    Let me know if you have any further problems.

    Geraldine Van der Auwera, PhD

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