[svtoolkit-help] Unable to execute QScript: CNVDiscoveryPipeline.script() threw the following exception: java.lang.N

[mehar <meh...@he...>]

Hi,

I am using the GenomeStrip version extracted from 
"svtoolkit_2.00.1572.tar.gz" . Taking the example from
http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_CNVDiscoveryPipeline.html 
, executed the following command:

|classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"

java-Xmx4g  -cp ${classpath}  \
org.broadinstitute.gatk.queue.QCommandLine  \
-S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath}  \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R canFam3.fa \
-genomeMaskFile mask.canFam3.fa
-I BC_Bams.list \
-md meta_directory \
-runDirectory CNV \
-jobLogDir CNV/logs \
-tilingWindowSize1000  \
-tilingWindowOverlap500  \
-maximumReferenceGapLength1000  \
-boundaryPrecision100  \
-minimumRefinedLength500  \
-run|

And have the following error:

|##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript:  Unable  to executeQScript:  CNVDiscoveryPipeline.script()  threw the following exception:  java.lang.NullPointerException
     at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159)
     at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147)
     at scala.collection.Iterator$class.foreach(Iterator.scala:727)
     at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
     at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
     at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
     at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:147)
     at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
     at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
     at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
     at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
Caused  by:  java.lang.NullPointerException
     atCNVDiscoveryPipeline.sequenceIntervalMap$lzycompute(CNVDiscoveryPipeline.q:59)
     atCNVDiscoveryPipeline.sequenceIntervalMap(CNVDiscoveryPipeline.q:55)
     atCNVDiscoveryPipeline.createStages(CNVDiscoveryPipeline.q:213)
     atCNVDiscoveryPipeline.script(CNVDiscoveryPipeline.q:97)
     at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156)
     ...  10  more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questionshttp://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Unable to execute QScript: CNVDiscoveryPipeline.script() threw the following exception: java.lang.NullPointerException
##### ERROR ------------------------------------------------------------------------------------------
INFO11:56:34,380  QCommandLine  -  Shutting  down jobs.  Please  wait...  |

Could someone help to fix this. Thanks.