NullPointerException in RealignerTargetCreator

Hi there,

I've encountered a NullPointerException when running RealignerTargetCreator. I wasn't able to find any hint that that's a known problem, so I'm posting it here (sorry, should I have overlooked something).

INFO  21:41:18,635 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  21:41:18,638 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.8-1-g932cd3a, Compiled 2013/12/06 16:47:15 
INFO  21:41:18,638 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  21:41:18,638 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  21:41:18,645 HelpFormatter - Program Args: -l INFO -R hg18/hg18.fasta -I aln/hiseq.wholegenome.cov30.stampy.sorted.markdup.bam -T RealignerTargetCreator -nt 12 -o aln/hiseq.wholegenome.cov30.stampy.indels.intervals 
INFO  21:41:18,645 HelpFormatter - Date/Time: 2014/02/24 21:41:18 
INFO  21:41:18,645 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  21:41:18,646 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  21:41:18,733 GenomeAnalysisEngine - Strictness is SILENT 
INFO  21:41:18,842 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
INFO  21:41:18,853 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:18,923 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07 
INFO  21:41:18,956 MicroScheduler - Running the GATK in parallel mode with 12 total threads, 1 CPU thread(s) for each of 12 data thread(s), of 24 processors available on this machine 
INFO  21:41:19,038 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  21:41:19,823 GenomeAnalysisEngine - Done preparing for traversal 
INFO  21:41:19,823 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  21:41:19,825 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining 
INFO  21:41:19,910 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:19,916 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 
INFO  21:41:19,919 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:19,928 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 
INFO  21:41:19,937 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:19,944 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 
INFO  21:41:19,944 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:19,951 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 
INFO  21:41:19,952 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:19,958 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 
INFO  21:41:19,958 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:19,964 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 
INFO  21:41:19,964 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:19,975 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 
INFO  21:41:19,976 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:19,980 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00 
INFO  21:41:19,980 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:19,984 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00 
INFO  21:41:19,985 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:19,989 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00 
INFO  21:41:19,990 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:41:20,010 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 
INFO  21:41:49,933 ProgressMeter -   chr1:26116497        2.60e+07   30.0 s        1.0 s      0.8%        59.0 m    58.5 m 
INFO  21:42:19,937 ProgressMeter -   chr1:57885373        5.77e+07   60.0 s        1.0 s      1.9%        53.2 m    52.2 m 
INFO  21:42:49,941 ProgressMeter -   chr1:88146121        8.80e+07   90.0 s        1.0 s      2.9%        52.4 m    50.9 m 
INFO  21:43:03,098 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.NullPointerException
        at org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState.getLocation(LocusIteratorByState.java:218)
        at org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:294)
        at org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:233)
        at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:70)
        at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
        at org.broadinstitute.sting.gatk.executive.WindowMaker$WindowMakerIterator.advance(WindowMaker.java:200)
        at org.broadinstitute.sting.gatk.executive.WindowMaker$WindowMakerIterator.hasNext(WindowMaker.java:169)
        at org.broadinstitute.sting.gatk.datasources.providers.LocusView.advance(LocusView.java:180)
        at org.broadinstitute.sting.gatk.datasources.providers.LocusView.hasNextLocus(LocusView.java:148)
        at org.broadinstitute.sting.gatk.datasources.providers.AllLocusView.advance(AllLocusView.java:127)
        at org.broadinstitute.sting.gatk.datasources.providers.AllLocusView.hasNext(AllLocusView.java:85)
        at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$MapDataIterator.hasNext(TraverseLociNano.java:167)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:268)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
        at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
        at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
        at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
        at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:98)
        at java.util.concurrent.FutureTask.run(FutureTask.java:262)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:744)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.8-1-g932cd3a):
##### 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 questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

Please let me know if there is more information I can provide.

Best, Tobi

Answers

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