Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

MalformedReadFilter

SystemSystem Posts: 226Administrator admin
edited July 2012 in Tool Bulletin

A new tool has been released!

Check out the documentation at MalformedReadFilter.

Comments

  • leukogenomleukogenom Posts: 9Member
    edited September 2012
    /usr/java/latest/bin/java -jar /home/hricikt/tools/gatk2_0/gatk2_0.jar -T IndelRealigner -I $bam_files_fullpath -R /home/hricikt/resources/ucsc.hg19.fasta -o $out_file_fullpath -targetIntervals $interval_files_fullpath -known /home/hricikt/resources/1000G_phase1.indels.hg19.vcf -known /home/hricikt/resources/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MalformedRead
    
    ##### ERROR stack trace 
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: **Duplicate definition of argument with full name: filter_mismatching_base_and_quals**
            at org.broadinstitute.sting.commandline.ArgumentDefinitions.add(ArgumentDefinitions.java:59)
            at org.broadinstitute.sting.commandline.ParsingEngine.addArgumentSource(ParsingEngine.java:136)
            at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:198)
            at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
            at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
    
    Post edited by Geraldine_VdAuwera on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,089Administrator, GATK Developer admin

    Please give some context for the problem you experience, or at least a full stack trace. Also, try without the read filter specified and see if the problem persists.

    Geraldine Van der Auwera, PhD

  • leukogenomleukogenom Posts: 9Member

    Running without read filter throws exception for malformed read with mismatching base quality.

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

    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Duplicate definition of argument with full name: filter_mismatching_base_and_quals at org.broadinstitute.sting.commandline.ArgumentDefinitions.add(ArgumentDefinitions.java:59) at org.broadinstitute.sting.commandline.ParsingEngine.addArgumentSource(ParsingEngine.java:136) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:198) 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 2.0-35-g2d70733):
    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: Duplicate definition of argument with full name: filter_mismatching_base_and_quals
    ERROR ------------------------------------------------------------------------------------------

    Is this the full stack trace? Thanks:)

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,089Administrator, GATK Developer admin

    Yes, that's better, thank you. This tells me what version you're using, and since you're using an older version, I can ask you to upgrade to the latest one. This looks like a bug that has been fixed -- but let me know if the problem persists after upgrading.

    Geraldine Van der Auwera, PhD

  • leukogenomleukogenom Posts: 9Member

    Got it thanks so much. Do I need to redo RealignerTargetCreator since my .intervals file was generated by the older version? Thanks again:)

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,089Administrator, GATK Developer admin

    You're welcome :)

    To be safe I would recommend rerunning the TargetCreator, yes. There shouldn't be much difference if any, but it's better practice.

    Geraldine Van der Auwera, PhD

  • leukogenomleukogenom Posts: 9Member

    I've downloaded the most recent version, re-ran RealignerTargetCreator and get the same error when attempting to apply the MalformedReadfilter to IndelRealigner. Leaving out the MalformedReadfilter causes gatk to blow up with execption due to mismatching base quality. I believe this filter worked in v1.6?

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

    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Duplicate definition of argument with full name: filter_mismatching_base_and_quals at org.broadinstitute.sting.commandline.ArgumentDefinitions.add(ArgumentDefinitions.java:59) at org.broadinstitute.sting.commandline.ParsingEngine.addArgumentSource(ParsingEngine.java:136) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:198) 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 2.1-10-gdbc86ec):
    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: Duplicate definition of argument with full name: filter_mismatching_base_and_quals
    ERROR ------------------------------------------------------------------------------------------

    ~

  • leukogenomleukogenom Posts: 9Member

    I'm sorry I forgot to mention that I used the same command from my first post here on Sept 27. Just changed the "gatk2_0" to "gatk2_1"... Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,089Administrator, GATK Developer admin

    OK, found the problem. The cmdline argument for this filter was renamed, now you need to call it with either -filterMBQ or --filter_mismatching_base_and_quals. Sorry I didn't catch this one sooner. In future, be sure to check in the docs that you have the right argument name.

    http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_filters_MalformedReadFilter.html

    Geraldine Van der Auwera, PhD

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