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Exception error on running Mutect2 "java.lang.NullPointerException"

Error Message:

java.lang.NullPointerException
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getContigNames(SequenceDictionaryUtils.java:463)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getCommonContigsByName(SequenceDictionaryUtils.java:457)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.compareDictionaries(SequenceDictionaryUtils.java:234)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:150)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:98)
at org.broadinstitute.hellbender.engine.GATKTool.validateSequenceDictionaries(GATKTool.java:701)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:643)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:156)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

Please help to me understand what is the issue

Tagged:

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Vithya

    Please send me the command you are using, the version of gat, the dataset you are using mutect2 on and the entire error log.
    Thank you.

    Regards
    Bhanu

  • VithyaVithya Member

    Hi @bhanuGandham,
    I am using GATK - v 4.0.9.0. And command used is ./gatk Mutect2 -R ~/NIPTER/wg.fa -I ~/NIPTER/SRR6676163.bam -tumor SRR6676163 -O sample.vcf .Dataset I used on mutect2 was taken from SRA with SRR ID - SRR6676163

    And the entire error log:

    _Using GATK jar /home/vithya/Documents/Variant_caller/gatk-4.0.9.0/gatk-package-4.0.9.0-local.jar
    Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/vithya/Documents/Variant_caller/gatk-4.0.9.0/gatk-package-4.0.9.0-local.jar Mutect2 -R /home/vithya/NIPTER/wg.fa -I /home/vithya/NIPTER/SRR6676163.bam -tumor SRR6676163 -O sample.vcf
    13:04:24.552 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/vithya/Documents/Variant_caller/gatk-4.0.9.0/gatk-package-4.0.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    13:04:26.655 INFO Mutect2 - ------------------------------------------------------------
    13:04:26.656 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.9.0
    13:04:26.656 INFO Mutect2 - For support and documentation go to
    13:04:26.657 INFO Mutect2 - Executing as [email protected] on Linux v4.15.0-36-generic amd64
    13:04:26.657 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v10.0.2+13-Ubuntu-1ubuntu0.18.04.2
    13:04:26.658 INFO Mutect2 - Start Date/Time: 24 October 2018 at 1:04:24 PM IST
    13:04:26.658 INFO Mutect2 - ------------------------------------------------------------
    13:04:26.658 INFO Mutect2 - ------------------------------------------------------------
    13:04:26.660 INFO Mutect2 - HTSJDK Version: 2.16.1
    13:04:26.660 INFO Mutect2 - Picard Version: 2.18.13
    13:04:26.660 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    13:04:26.660 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    13:04:26.661 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    13:04:26.661 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    13:04:26.661 INFO Mutect2 - Deflater: IntelDeflater
    13:04:26.661 INFO Mutect2 - Inflater: IntelInflater
    13:04:26.661 INFO Mutect2 - GCS max retries/reopens: 20
    13:04:26.661 INFO Mutect2 - Requester pays: disabled
    13:04:26.662 INFO Mutect2 - Initializing engine
    13:04:26.967 INFO Mutect2 - Shutting down engine
    [24 October 2018 at 1:04:26 PM IST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.04 minutes.
    Runtime.totalMemory()=156237824
    java.lang.NullPointerException
    at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getContigNames(SequenceDictionaryUtils.java:463)
    at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.getCommonContigsByName(SequenceDictionaryUtils.java:457)
    at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.compareDictionaries(SequenceDictionaryUtils.java:234)
    at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:150)
    at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:98)
    at org.broadinstitute.hellbender.engine.GATKTool.validateSequenceDictionaries(GATKTool.java:701)
    at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:643)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:156)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)
    _

    Thanks

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Vithya

    Would you please do a BAM file diagnosis by running ValidateSamFile . Please post the results of that here so we can figure out what the issue maybe here. Also you can follow this link for more information on fixing BAM related issue.

    Regards
    Bhanu

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