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RealignerTargetCreator

I am using GenomeAnalysisTK-3.4-46 on my linux machine. After using following command for Realigner Target Creator

Java -d64 -Xmx4g -jar /home/nikki/GenomeAnalysisTK-3.4-46/GenomeAnalysisTK.jar -T RealignerTargetCreator -R ./../humangenome/ucsc/ucsc.hg19.fasta -I bowtieresult_3_new/output_new.marked.bam -o test.list

I get the following error.
INFO 16:30:17,102 HelpFormatter - Executing as [email protected] on Linux 3.13.0-71-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b02.
INFO 16:30:17,102 HelpFormatter - Date/Time: 2015/12/16 16:30:17
INFO 16:30:17,102 HelpFormatter - ---------------------------------------------------------------------------------
INFO 16:30:17,102 HelpFormatter - ---------------------------------------------------------------------------------
INFO 16:30:17,141 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:30:17,336 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 16:30:17,344 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 16:30:17,410 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
INFO 16:30:17,481 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 16:30:17,576 GenomeAnalysisEngine - Done preparing for traversal
INFO 16:30:17,577 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 16:30:17,577 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 16:30:17,577 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 16:30:18,715 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.IllegalArgumentException: Negative position
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:707)
at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:202)
at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:329)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:150)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.(LocusReferenceView.java:126)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:90)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, 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: Negative position
ERROR ------------------------------------------------------------------------------------------

After using -known parameter I still get the following error message

INFO 17:37:33,181 HelpFormatter - Executing as [email protected] on Linux 3.13.0-71-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b02.
INFO 17:37:33,181 HelpFormatter - Date/Time: 2015/12/16 17:37:33
INFO 17:37:33,181 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:37:33,181 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:37:33,220 GenomeAnalysisEngine - Strictness is SILENT
INFO 17:37:33,339 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 17:37:33,345 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 17:37:33,378 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
INFO 17:37:33,593 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 17:37:33,671 GenomeAnalysisEngine - Done preparing for traversal
INFO 17:37:33,671 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 17:37:33,672 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 17:37:33,672 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 17:37:34,931 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.IllegalArgumentException: Negative position
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:707)
at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:202)
at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:329)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:150)
at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.(LocusReferenceView.java:126)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:90)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, 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: Negative position
ERROR ------------------------------------------------------------------------------------------

I am not sure if this is Bug or error by me. Any suggestion would be helpful.
Thanks!

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @nikkinath
    Hi,

    I think this was a bug that has been fixed in the latest version. If you upgrade to the latest version, you should not get the error.

    -Sheila

  • nikkinathnikkinath GermanyMember

    @Sheila

    Thanks for your suggestion. I used GATK version 3.5-0 and still get the same error message. I used following code:

    java -Xmx4g -jar /home/nikki/GATK/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /ucsc/ucsc.hg19.fasta -known /broadinstitute/dbsnp_138.hg19.excluding_sites_after_129.vcf -o realign.list -I output_bowtieoutput.duplicated.bam

    INFO 16:18:54,912 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
    INFO 16:18:55,161 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
    INFO 16:18:55,288 GenomeAnalysisEngine - Done preparing for traversal
    INFO 16:18:55,289 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 16:18:55,289 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 16:18:55,289 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
    INFO 16:18:56,580 GATKRunReport - Uploaded run statistics report to AWS S3

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

    java.lang.IllegalArgumentException: Negative position
    at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:707)
    at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:205)
    at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:343)
    at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:163)
    at org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceView.(LocusReferenceView.java:139)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:90)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    ERROR
    ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ERROR If not, please post the error message, 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: Negative position
    ERROR ------------------------------------------------------------------------------------------

    Any suggestion??

    Thanks!

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