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Gatk Baserecalibrator Error

After mark duplicate step using picard i added read groups to bam file and now i am trying to run baserecalibrator using gatk. i am getting following error

chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:169)
at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:98)
at org.broadinstitute.hellbender.engine.GATKTool.validateSequenceDictionaries(GATKTool.java:709)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:643)
at org.broadinstitute.hellbender.engine.ReadWalker.onStartup(ReadWalker.java:50)
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)


this is my command-
gatk BaseRecalibrator -R hg38.fa -I input.bam -known-sites dbsnp_138.hg19.vcf -O output.bam

Could you please me to resolve this error. Thank you in advance.

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @DrVenkat

    I do not see the error here, could you please post the entire log and the version of GTAK you are using.

    Also from the command i see that you are using a hg38 reference against a hg19 knownsites vcf. That could be one of the reasons you see an error.

  • DrVenkatDrVenkat Member
    hi,
    sorry for the confusion i am using hg19 reference against hg19 knownsites vcf.

    14:57:13.300 INFO ProgressMeter - chrX:111078152 15.4 36076000 2349702.5
    14:57:23.303 INFO ProgressMeter - chrX:123540206 15.5 36582000 2357062.3
    14:57:33.305 INFO ProgressMeter - chrX:135288528 15.7 37095000 2364717.0
    14:57:43.323 INFO ProgressMeter - chrX:152991293 15.9 37587000 2370846.2
    14:57:53.334 INFO ProgressMeter - chr6_cox_hap2:3260547 16.0 38095000 2377863.6
    14:58:01.491 INFO BaseRecalibrator - 7436007 read(s) filtered by: ((((((MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND WellformedReadFilter)
    7436007 read(s) filtered by: (((((MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter)
    7436007 read(s) filtered by: ((((MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter)
    204926 read(s) filtered by: (((MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter)
    204926 read(s) filtered by: ((MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter)
    204926 read(s) filtered by: (MappingQualityNotZeroReadFilter AND MappingQualityAvailableReadFilter)
    204926 read(s) filtered by: MappingQualityNotZeroReadFilter
    7231081 read(s) filtered by: NotDuplicateReadFilter

    14:58:01.491 INFO ProgressMeter - chrUn_gl000244:12383 16.2 38541677 2385501.7
    14:58:01.491 INFO ProgressMeter - Traversal complete. Processed 38541677 total reads in 16.2 minutes.
    14:58:01.551 INFO BaseRecalibrator - Calculating quantized quality scores...
    14:58:01.564 INFO BaseRecalibrator - Writing recalibration report...
    14:58:01.829 INFO BaseRecalibrator - ...done!
    14:58:01.830 INFO BaseRecalibrator - Shutting down engine
    [15 January, 2019 2:58:01 PM IST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 16.20 minutes.
    Runtime.totalMemory()=2129133568
    Tool returned:
    38541677
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @DrVenkat

    The output you see while running a command is the job-summary info on System.err. It is not an error.
    If you do not want to see this you can use this option in your command: --QUIET.
    I hope this helps.

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