GATK error

Hi,all; When I run the following command
/bin/java/jre1.7.0_55/bin/java -Xmx2G -Djava.io.tmpdir=./java_tmp -jar /bin/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /Database/human_19/hg19_fasta_GATK/hg19.fasta \
-I ./results/sample1/sample1.sort.rmdup.bam \
-L /Database/CallVariantRegion/ex_region.sort.chr1.bed \
-B:dbsnp,VCF /Database/GATK_DB_HG19/dbsnp_132.hg19.vcf \
-o ./results/CK-TUM/GATK/snp/chr1.raw.snp.vcf \
-stand_call_conf 50 -stand_emit_conf 10.0 \
-A DepthOfCoverage -A RMSMappingQuality -baq CALCULATE_AS_NECESSARY && \

Then a error below happened, Please help me, thanks

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Argument with name 'B' isn't defined.
ERROR ------------------------------------------------

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    You are using command line arguments that are very old. Please check the documentation for updated usage of the tools you want to use.

  • JintuWangJintuWang SZMember

    When I replace the Argument with name 'B' to 'D' ,then another error happened ,see the following meaning the usage of version

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
    ERROR
    ERROR This means that one or more arguments or inputs in your command are incorrect.
    ERROR The error message below tells you what is the problem.
    ERROR
    ERROR If the problem is an invalid argument, please check the online documentation guide
    ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ERROR
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ERROR
    ERROR MESSAGE: Annotation DepthOfCoverage is no longer available in the GATK; it has been deprecated since version 2.4 (renamed to Coverage)
    ERROR ------------------------------------------------------------------------------------------
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Right, so you need to replace -A DepthOfCoverage by -A Coverage.

  • JintuWangJintuWang SZMember

    Before,I have used the version 1.0.6076,but a error happened, see the following,thanks, I don't know what it means,
    So I try to use the version GenomeAnalysisTK-3.3-0, but some paremeter have been deprecated

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

    java.lang.ArrayIndexOutOfBoundsException: 68
    at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:156)
    at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:244)
    at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:535)
    at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:588)
    at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:523)
    at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:656)
    at org.broadinstitute.sting.utils.baq.BAQSamIterator.next(BAQSamIterator.java:52)
    at org.broadinstitute.sting.utils.baq.BAQSamIterator.next(BAQSamIterator.java:16)
    at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:106)
    at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.(CountingFilteringIterator.java:59)
    at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.applyDecoratingIterators(SAMDataSource.java:658)
    at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.getIterator(SAMDataSource.java:567)
    at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.seek(SAMDataSource.java:512)
    at org.broadinstitute.sting.gatk.executive.MicroScheduler.getReadIterator(MicroScheduler.java:214)
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:59)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 1.0.6076):
    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: 68
    ERROR ------------------------------------------------------------------------------------------
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @JintuWang
    Hi,

    The error message you posted is from a very old version of GATK. We cannot help you with those errors. Please try using the latest version and let us know if there is still an error.

    Thanks,
    Sheila

  • JintuWangJintuWang SZMember

    OK, I have solved the problem. Thanks

Sign In or Register to comment.