Scala is a combination of an object oriented framework and a functional programming language. For a good introduction see the free online book Programming Scala.
The following are extremely brief answers to frequently asked questions about Scala which often pop up when first viewing or editing QScripts. For more information on Scala there a multitude of resources available around the web including the Scala home page and the online Scala Doc.
var and val?var is a value you can later modify, while val is similar to final in Java.
Because the GATK and Queue are a mix of Scala and Java sometimes you'll run into problems when you need a Scala collection and instead a Java collection is returned.
MyQScript.scala:39: error: type mismatch;
found : java.util.List[java.lang.String]
required: scala.List[String]
val wrapped: List[String] = TextFormattingUtils.wordWrap(text, width)
Use the implicit definitions in JavaConversions to automatically convert the basic Java collections to and from Scala collections.
import collection.JavaConversions._
Scala has a very rich collections framework which you should take the time to enjoy. One of the first things you'll notice is that the default Scala collections are immutable, which means you should treat them as you would a String. When you want to 'modify' an immutable collection you need to capture the result of the operation, often assigning the result back to the original variable.
var str = "A"
str + "B"
println(str) // prints: A
str += "C"
println(str) // prints: AC
var set = Set("A")
set + "B"
println(set) // prints: Set(A)
set += "C"
println(set) // prints: Set(A, C)
Use the :+ operator for a single value.
var myList = List.empty[String]
myList :+= "a"
myList :+= "b"
myList :+= "c"
Use ++ for appending a list.
var myList = List.empty[String]
myList ++= List("a", "b", "c")
Use the + operator.
var mySet = Set.empty[String]
mySet += "a"
mySet += "b"
mySet += "c"
Use the + and -> operators.
var myMap = Map.empty[String,Int]
myMap += "a" -> 1
myMap += "b" -> 2
myMap += "c" -> 3
Option is a Scala generic type that can either be some generic value or None. Queue often uses it to represent primitives that may be null.
var myNullableInt1: Option[Int] = Some(1)
var myNullableInt2: Option[Int] = None
François Armand's slide deck is a good introduction: http://www.slideshare.net/normation/scala-dreaded
To quote from his slides:
Give me a variable name but
- I don't care of what it is
- and/or
- don't want to pollute my namespace with it
Use the .format() method.
This Java snippet:
String formatted = String.format("%s %i", myString, myInt);
In Scala would be:
val formatted = "%s %i".format(myString, myInt)
No. Currently Scala's Enumeration class does not interact with the Java reflection API in a way that could be used for Queue command line arguments. You can use Java enums if for example you are importing a Java based walker's enum type.
If/when we find a workaround for Queue we'll update this entry. In the meantime try using a String.
At the Broad, we typically put it somewhere like this:
/home/radon01/depristo/work/local/scala-2.7.5.final
Next, create a symlink from this directory to trunk/scala/installation:
ln -s /home/radon01/depristo/work/local/scala-2.7.5.final trunk/scala/installation
Right now the only way to get scala walkers into the GATK is by explicitly setting your CLASSPATH in your .my.cshrc file:
setenv CLASSPATH /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/FourBaseRecaller.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/Playground.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/StingUtils.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/bcel-5.2.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/colt-1.2.0.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/google-collections-0.9.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/javassist-3.7.ga.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/junit-4.4.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/log4j-1.2.15.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/picard-1.02.63.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/picard-private-875.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/reflections-0.9.2.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/sam-1.01.63.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/simple-xml-2.0.4.jar:/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GATKScala.jar:/humgen/gsa-scr1/depristo/local/scala-2.7.5.final/lib/scala-library.jar
Really this needs to be manually updated whenever any of the libraries are updated. If you see this error:
Caused by: java.lang.RuntimeException: java.util.zip.ZipException: error in opening zip file
at org.reflections.util.VirtualFile.iterable(VirtualFile.java:79)
at org.reflections.util.VirtualFile$5.transform(VirtualFile.java:169)
at org.reflections.util.VirtualFile$5.transform(VirtualFile.java:167)
at org.reflections.util.FluentIterable$3.transform(FluentIterable.java:43)
at org.reflections.util.FluentIterable$3.transform(FluentIterable.java:41)
at org.reflections.util.FluentIterable$ForkIterator.computeNext(FluentIterable.java:81)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:132)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:127)
at org.reflections.util.FluentIterable$FilterIterator.computeNext(FluentIterable.java:102)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:132)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:127)
at org.reflections.util.FluentIterable$TransformIterator.computeNext(FluentIterable.java:124)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:132)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:127)
at org.reflections.Reflections.scan(Reflections.java:69)
at org.reflections.Reflections.<init>(Reflections.java:47)
at org.broadinstitute.sting.utils.PackageUtils.<clinit>(PackageUtils.java:23)
It's because the libraries aren't updated. Basically just do an ls of your trunk/dist directory after the GATK has been build, make this your classpath as above, and tack on:
/humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GATKScala.jar:/humgen/gsa-scr1/depristo/local/scala-2.7.5.final/lib/scala-library.jar
A command that almost works (but you'll need to replace the spaces with colons) is:
#setenv CLASSPATH $CLASSPATH `ls /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/*.jar` /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GATKScala.jar:/humgen/gsa-scr1/depristo/local/scala-2.7.5.final/lib/scala-library.jar
All of the Scala source code lives in scala/src, which you build using ant scala
There are already some example Scala walkers in scala/src, so doing a standard checkout, installing scala, settting up your environment, should allow you to run something like:
gsa2 ~/dev/GenomeAnalysisTK/trunk > ant scala
Buildfile: build.xml
init.scala:
scala:
[echo] Sting: Compiling scala!
[scalac] Compiling 2 source files to /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/scala/classes
[scalac] warning: there were deprecation warnings; re-run with -deprecation for details
[scalac] one warning found
[scalac] Compile suceeded with 1 warning; see the compiler output for details.
[delete] Deleting: /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GATKScala.jar
[jar] Building jar: /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/dist/GATKScala.jar
Until we can include Scala walkers along with the main GATK jar (avoiding the classpath issue too) you have to invoke your scala walkers using this syntax:
java -Xmx2048m org.broadinstitute.sting.gatk.CommandLineGATK -T BaseTransitionTableCalculator -R /broad/1KG/reference/human_b36_both.fasta -I /broad/1KG/DCC_merged/freeze5/NA12878.pilot2.SLX.bam -l INFO -L 1:1-100
Here, the BaseTransitionTableCalculator walker is written in Scala and being loaded into the system by the GATK walker manager. Otherwise everything looks like a normal GATK module.
Hi, folks,
I am trying my queue scala scripts, often get error message:
Conflicting collector combinations in option list; please refer to the release notes for the combinations allowed
However, from the debug information, the command line looks correct (?):
ERROR 12:07:05,460 FunctionEdge - Error: 'java' '-Xmx8192m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/Users/wxing/TPU/run/.queue/tmp' '-cp' '/Users/wxing/TPU/gatk/dist/Queue.jar' 'net.sf.picard.sam.SortSam' 'INPUT=/Users/wxing/TPU/run/SRR064286_1.fastq.aligned.sam' 'TMP_DIR=/Users/wxing/TPU/run/.queue/tmp' 'OUTPUT=/Users/wxing/TPU/run/SRR064286_1.fastq.aligned.bam' 'VALIDATION_STRINGENCY=SILENT' 'SO=coordinate' 'CREATE_INDEX=true'
Anyone had similar issues? any tricks for debugging?
Many thanks, Wei
In addition to testing walkers individually, you may want to also run integration tests for your QScript pipelines.
ant target pipelinetest and run under pipelinetestrun.PipelineTest to run under the ant target.PipelineTestSpec and then run it via PipelineTest.exec().When building up a pipeline test spec specify the following variables for your test.
| Variable | Type | Description |
|---|---|---|
args |
String |
The arguments to pass to the Queue test, ex: -S scala/qscript/examples/HelloWorld.scala |
jobQueue |
String |
Job Queue to run the test. Default is null which means use hour. |
fileMD5s |
Map[Path, MD5] |
Expected MD5 results for each file path. |
expectedException |
classOf[Exception] |
Expected exception from the test. |
The following example runs the ExampleCountLoci QScript on a small bam and verifies that the MD5 result is as expected.
It is checked into the Sting repository under scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
package org.broadinstitute.sting.queue.pipeline.examples
import org.testng.annotations.Test
import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
import org.broadinstitute.sting.BaseTest
class ExampleCountLociPipelineTest {
@Test
def testCountLoci {
val testOut = "count.out"
val spec = new PipelineTestSpec
spec.name = "countloci"
spec.args = Array(
" -S scala/qscript/examples/ExampleCountLoci.scala",
" -R " + BaseTest.hg18Reference,
" -I " + BaseTest.validationDataLocation + "small_bam_for_countloci.bam",
" -o " + testOut).mkString
spec.fileMD5s += testOut -> "67823e4722495eb10a5e4c42c267b3a6"
PipelineTest.executeTest(spec)
}
}
To test if the script is at least compiling with your arguments run ant pipelinetest specifying the name of your class to -Dsingle:
ant pipelinetest -Dsingle=ExampleCountLociPipelineTest
Sample output:
[testng] --------------------------------------------------------------------------------
[testng] Executing test countloci with Queue arguments: -S scala/qscript/examples/ExampleCountLoci.scala -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -I /humgen/gsa-hpprojects/GATK/data/Validation_Data/small_bam_for_countloci.bam -o count.out -bsub -l WARN -tempDir pipelinetests/countloci/temp/ -runDir pipelinetests/countloci/run/ -jobQueue hour
[testng] => countloci PASSED DRY RUN
[testng] PASSED: testCountLoci
As of July 2011 the pipeline tests run against LSF 7.0.6 and Grid Engine 6.2u5. To include these two packages in your environment use the hidden dotkit .combined_LSF_SGE.
reuse .combined_LSF_SGE
Once you are satisfied that the dry run has completed without error, to actually run the pipeline test run ant pipelinetestrun.
ant pipelinetestrun -Dsingle=ExampleCountLociPipelineTest
Sample output:
[testng] --------------------------------------------------------------------------------
[testng] Executing test countloci with Queue arguments: -S scala/qscript/examples/ExampleCountLoci.scala -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -I /humgen/gsa-hpprojects/GATK/data/Validation_Data/small_bam_for_countloci.bam -o count.out -bsub -l WARN -tempDir pipelinetests/countloci/temp/ -runDir pipelinetests/countloci/run/ -jobQueue hour -run
[testng] ##### MD5 file is up to date: integrationtests/67823e4722495eb10a5e4c42c267b3a6.integrationtest
[testng] Checking MD5 for pipelinetests/countloci/run/count.out [calculated=67823e4722495eb10a5e4c42c267b3a6, expected=67823e4722495eb10a5e4c42c267b3a6]
[testng] => countloci PASSED
[testng] PASSED: testCountLoci
If you don't know the MD5s yet you can run the command yourself on the command line and then MD5s the outputs yourself, or you can set the MD5s in your test to "" and run the pipeline.
When the MD5s are blank as in:
spec.fileMD5s += testOut -> ""
You run:
ant pipelinetest -Dsingle=ExampleCountLociPipelineTest -Dpipeline.run=run
And the output will look like:
[testng] --------------------------------------------------------------------------------
[testng] Executing test countloci with Queue arguments: -S scala/qscript/examples/ExampleCountLoci.scala -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -I /humgen/gsa-hpprojects/GATK/data/Validation_Data/small_bam_for_countloci.bam -o count.out -bsub -l WARN -tempDir pipelinetests/countloci/temp/ -runDir pipelinetests/countloci/run/ -jobQueue hour -run
[testng] ##### MD5 file is up to date: integrationtests/67823e4722495eb10a5e4c42c267b3a6.integrationtest
[testng] PARAMETERIZATION[countloci]: file pipelinetests/countloci/run/count.out has md5 = 67823e4722495eb10a5e4c42c267b3a6, stated expectation is , equal? = false
[testng] => countloci PASSED
[testng] PASSED: testCountLoci
When a pipeline test fails due to an MD5 mismatch you can use the MD5 database to diff the results.
[testng] --------------------------------------------------------------------------------
[testng] Executing test countloci with Queue arguments: -S scala/qscript/examples/ExampleCountLoci.scala -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -I /humgen/gsa-hpprojects/GATK/data/Validation_Data/small_bam_for_countloci.bam -o count.out -bsub -l WARN -tempDir pipelinetests/countloci/temp/ -runDir pipelinetests/countloci/run/ -jobQueue hour -run
[testng] ##### Updating MD5 file: integrationtests/67823e4722495eb10a5e4c42c267b3a6.integrationtest
[testng] Checking MD5 for pipelinetests/countloci/run/count.out [calculated=67823e4722495eb10a5e4c42c267b3a6, expected=67823e4722495eb10a5e0000deadbeef]
[testng] ##### Test countloci is going fail #####
[testng] ##### Path to expected file (MD5=67823e4722495eb10a5e0000deadbeef): integrationtests/67823e4722495eb10a5e0000deadbeef.integrationtest
[testng] ##### Path to calculated file (MD5=67823e4722495eb10a5e4c42c267b3a6): integrationtests/67823e4722495eb10a5e4c42c267b3a6.integrationtest
[testng] ##### Diff command: diff integrationtests/67823e4722495eb10a5e0000deadbeef.integrationtest integrationtests/67823e4722495eb10a5e4c42c267b3a6.integrationtest
[testng] FAILED: testCountLoci
[testng] java.lang.AssertionError: 1 of 1 MD5s did not match.
If you need to examine a number of MD5s which may have changed you can briefly shut off MD5 mismatch failures by setting parameterize = true.
spec.parameterize = true
spec.fileMD5s += testOut -> "67823e4722495eb10a5e4c42c267b3a6"
For this run:
ant pipelinetest -Dsingle=ExampleCountLociPipelineTest -Dpipeline.run=run
If there's a match the output will resemble:
[testng] --------------------------------------------------------------------------------
[testng] Executing test countloci with Queue arguments: -S scala/qscript/examples/ExampleCountLoci.scala -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -I /humgen/gsa-hpprojects/GATK/data/Validation_Data/small_bam_for_countloci.bam -o count.out -bsub -l WARN -tempDir pipelinetests/countloci/temp/ -runDir pipelinetests/countloci/run/ -jobQueue hour -run
[testng] ##### MD5 file is up to date: integrationtests/67823e4722495eb10a5e4c42c267b3a6.integrationtest
[testng] PARAMETERIZATION[countloci]: file pipelinetests/countloci/run/count.out has md5 = 67823e4722495eb10a5e4c42c267b3a6, stated expectation is 67823e4722495eb10a5e4c42c267b3a6, equal? = true
[testng] => countloci PASSED
[testng] PASSED: testCountLoci
While for a mismatch it will look like this:
[testng] --------------------------------------------------------------------------------
[testng] Executing test countloci with Queue arguments: -S scala/qscript/examples/ExampleCountLoci.scala -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -I /humgen/gsa-hpprojects/GATK/data/Validation_Data/small_bam_for_countloci.bam -o count.out -bsub -l WARN -tempDir pipelinetests/countloci/temp/ -runDir pipelinetests/countloci/run/ -jobQueue hour -run
[testng] ##### MD5 file is up to date: integrationtests/67823e4722495eb10a5e4c42c267b3a6.integrationtest
[testng] PARAMETERIZATION[countloci]: file pipelinetests/countloci/run/count.out has md5 = 67823e4722495eb10a5e4c42c267b3a6, stated expectation is 67823e4722495eb10a5e0000deadbeef, equal? = false
[testng] => countloci PASSED
[testng] PASSED: testCountLoci
Hi there, I wanted to reproduce in my variant calling Queue script the same conditional you have in MethodsDevelopmenCallingPipeline, i.e. including InbreedingCoeff depending on the number of samples. However, in that script the number of samples is passed to the Target object as an integer, and I would like to count it from the bam file list passed as an input to the script.
Therefore I followed the method in DataProcessingPipeline, i.e.
import org.broadinstitute.sting.queue.util.QScriptUtils
[...]
@Input(doc="input BAM file - or list of BAM files", fullName="input", shortName="I", required=true)
var bamFile: File = _
[...]
val bamFilesList = QScriptUtils.createSeqFromFile(bamFile)
val sampleNo = bamFilesList.size
But unfortunately, despite DataProcessingPipeline works just fine, when I put these lines in my other script I get the following error:
INFO 12:48:08,616 HelpFormatter - Date/Time: 2012/11/08 12:48:08
INFO 12:48:08,616 HelpFormatter - ----------------------------------------------------------------------
INFO 12:48:08,616 HelpFormatter - ----------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException: Could not create module HaplotypeCallerStep because Cannot instantiate class (Invocation failure) caused by exception null
at org.broadinstitute.sting.utils.classloader.PluginManager.createByType(PluginManager.java:306)
at org.broadinstitute.sting.utils.classloader.PluginManager.createAllTypes(PluginManager.java:317)
at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:126)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
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 2.2-2-gf44cc4e):
##### 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: Could not create module HaplotypeCallerStep because Cannot instantiate class (Invocation failure) caused by exception null
##### ERROR ------------------------------------------------------------------------------------------
I tried several alternatives looking at the imports in DataProcessingPipeline but maybe I am missing something. Could you please advise?
thanks very much Francesco
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,