Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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.

Sign In or Register to comment.