Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

NullPointerException in PhaseByTransmission

nodrogluapnodrogluap Posts: 3Member
edited January 2013 in Ask the team

Hi all,

Has anyone else gotten the following:

java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(PhaseByTransmission.java:242) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:306) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:35) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:149) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

My command line was: java -jar GenomeAnalysisTK.jar -T PhaseByTransmission -V w01.sorted.vcf -o w01.phased.vcf -f "mom+dad=child" -R hg19.fa

Cheers,

Paul

Post edited by Geraldine_VdAuwera on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,276Administrator, GSA Member admin

    Hi Paul, can you specify which version of GATK you are using? Ideally we would prefer to have the full stack trace, not just a cutout of the error message.

    Geraldine Van der Auwera, PhD

  • nodrogluapnodrogluap Posts: 3Member

    Hi Geraldine,

    The version is v1.2-29-g0acaf2d.

    Here the full output...

    INFO 17:34:16,946 HelpFormatter - --------------------------------------------------------------------------------- INFO 17:34:16,949 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.2-29-g0acaf2d, Compiled 2011/09/29 00:21:43 INFO 17:34:16,949 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 17:34:16,950 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 17:34:16,950 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 17:34:16,950 HelpFormatter - Program Args: -T PhaseByTransmission -V w01.sorted.vcf -o w01.phased.vcf -f dad+mom=child -R /home/gordonp/ngs_utils/dbs/hg19_revised.fa
    INFO 17:34:16,950 HelpFormatter - Date/Time: 2012/09/05 17:34:16 INFO 17:34:16,951 HelpFormatter - --------------------------------------------------------------------------------- INFO 17:34:16,951 HelpFormatter - --------------------------------------------------------------------------------- INFO 17:34:16,959 RodBindingArgumentTypeDescriptor - Dynamically determined type of w01.sorted.vcf to be VCF INFO 17:34:16,965 GenomeAnalysisEngine - Strictness is SILENT INFO 17:34:17,076 RMDTrackBuilder - Loading Tribble index from disk for file w01.sorted.vcf

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(PhaseByTransmission.java:242) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:306) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:35) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:149) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 1.2-29-g0acaf2d):
    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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
    ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
    ERROR
    ERROR MESSAGE: Code exception (see stack trace for error itself)
    ERROR ------------------------------------------------------------------------------------------
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,276Administrator, GSA Member admin

    Thanks Paul, we'll look into it.

    Geraldine Van der Auwera, PhD

  • ebanksebanks Posts: 671GSA Member mod

    Hi Paul,

    You'll need to update to the latest version of the GATK. You are using an extremely old version.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • nodrogluapnodrogluap Posts: 3Member

    Hi,

    I still get a NPE (albeit a different one) with version 2.1-8:

    INFO 08:55:05,825 HelpFormatter - -------------------------------------------------------------------------------- INFO 08:55:05,827 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-8-g5efb575, Compiled 2012/08/30 14:22:17 INFO 08:55:05,827 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 08:55:05,828 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 08:55:05,828 HelpFormatter - Program Args: -T PhaseByTransmission -V w01.sorted.vcf -o w01.phased.vcf -ped trio_male.ped -R /home/gordonp/ngs_utils/dbs/hg19_revised.fa INFO 08:55:05,828 HelpFormatter - Date/Time: 2012/09/06 08:55:05 INFO 08:55:05,829 HelpFormatter - -------------------------------------------------------------------------------- INFO 08:55:05,829 HelpFormatter - -------------------------------------------------------------------------------- INFO 08:55:05,838 ArgumentTypeDescriptor - Dynamically determined type of w01.sorted.vcf to be VCF INFO 08:55:05,843 GenomeAnalysisEngine - Strictness is SILENT INFO 08:55:05,948 RMDTrackBuilder - Loading Tribble index from disk for file w01.sorted.vcf WARN 08:55:06,005 VCFStandardHeaderLines$Standards - Repairing standard header line for field GQ because -- type disagree; header has Float but standard is Integer -- descriptions disagree; header has 'Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype' but standard is 'Genotype Quality' WARN 08:55:06,005 VCFStandardHeaderLines$Standards - Repairing standard header line for field AC because -- count types disagree; header has UNBOUNDED but standard is A -- descriptions disagree; header has 'Allele count in genotypes' but standard is 'Allele count in genotypes, for each ALT allele, in the same order as listed' INFO 08:55:06,015 PedReader - Reading PED file trio_male.ped with missing fields: [] INFO 08:55:06,137 PedReader - Phenotype is other? false INFO 08:55:07,709 GATKRunReport - Uploaded run statistics report to AWS S3

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.getLikelihoodsAsMapSafeNull(PhaseByTransmission.java:551) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(PhaseByTransmission.java:585) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:799) at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.map(PhaseByTransmission.java:77) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:65) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:265) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.1-8-g5efb575):
    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: Code exception (see stack trace for error itself)
    ERROR ------------------------------------------------------------------------------------------
  • ebanksebanks Posts: 671GSA Member mod

    Ah, I see what's going on. The tool is expecting genotype likelihoods (PLs preferably, but if not then GLs) associated with each sample but your VCF must not have them. I'll patch the tool for the next major release to skip such sites in the future, but I expect that in the meantime you'll need to regenerate your VCF if there are no PLs at all or remove those records that don't have them.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • ebanksebanks Posts: 671GSA Member mod

    Actually, quick correction: in the next release these sites won't be skipped, but they'll be treated as having flat likelihoods.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

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