NullPointerException in RealignerTargetCreator

tobiasmarschalltobiasmarschall Saarbrücken, GermanyPosts: 2Member

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

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    Hi Tobi,

    I see you're using Stampy aligner; I seem to recall we've had other users who experienced issues with Stampy's output. Does your bam file validate with Picard?

    Though considering the stack trace, it could be an issue with multithreading. Does the issue persist when you run single-threaded?

    Geraldine Van der Auwera, PhD

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