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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!
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GATK error
JintuWang
SZMember ✭
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
Answers
You are using command line arguments that are very old. Please check the documentation for updated usage of the tools you want to use.
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 ------------------------------------------------------------------------------------------
Right, so you need to replace -A DepthOfCoverage by -A Coverage.
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 ------------------------------------------------------------------------------------------
@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
OK, I have solved the problem. Thanks