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"ERROR MESSAGE: Rod span 1:1-249250621 isn't contained..." while running the HaplotypeCaller

ChrisRandsChrisRands SwizerlandMember
edited August 2016 in Ask the GATK team

When I try to run the HaplotypeCaller I get this error below. Although I have searched the forum and elsewhere for solutions, I cannot solve the issue.

I get "No Errors found" when I run picard.jar ValidateSamFile. I am including all chromosomes in my reference, which I downloaded from ftp://ftp.broadinstitute.org/bundle/2.8/hg19/ . The only change I made to the reference was to remove the "chr" prefix from the chromosome names using sed (to make it consistent with my bam file), and I then regenerated the .fai and .dict files using samtools faidx and picard.jar CreateSequenceDictionary.

I'd be very grateful for your help. Thank you,
Chris

$ java -jar ~/scripts/GATK/GenomeAnalysisTK.jar -R hg19_broad_ftp/ucsc.hg19.noChrPrefix.fasta -T HaplotypeCaller -I ../aln.sorted.matePairfixed.bam -o aln.sorted.HaploTypeCaller.vcf
INFO 18:45:41,895 HelpFormatter - --------------------------------------------------------------------------------
INFO 18:45:41,897 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29
INFO 18:45:41,897 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 18:45:41,897 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO 18:45:41,898 HelpFormatter - [Tue Aug 23 18:45:41 CEST 2016] Executing on Linux 4.6.2-1-ARCH i386
INFO 18:45:41,898 HelpFormatter - Java HotSpot(TM) Server VM 1.8.0_101-b13 JdkDeflater
INFO 18:45:41,901 HelpFormatter - Program Args: -R hg19_broad_ftp/ucsc.hg19.noChrPrefix.fasta -T HaplotypeCaller -I ../aln.sorted.matePairfixed.bam -o aln.sorted.HaploTypeCaller.vcf
INFO 18:45:41,904 HelpFormatter - Executing as rands@bee on Linux 4.6.2-1-ARCH i386; Java HotSpot(TM) Server VM 1.8.0_101-b13.
INFO 18:45:41,904 HelpFormatter - Date/Time: 2016/08/23 18:45:41
INFO 18:45:41,904 HelpFormatter - --------------------------------------------------------------------------------
INFO 18:45:41,904 HelpFormatter - --------------------------------------------------------------------------------
INFO 18:45:41,919 GenomeAnalysisEngine - Strictness is SILENT
INFO 18:45:41,996 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
INFO 18:45:42,002 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 18:45:42,025 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO 18:45:42,037 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
INFO 18:45:42,103 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 18:45:42,144 GenomeAnalysisEngine - Done preparing for traversal
INFO 18:45:42,145 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 18:45:42,145 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 18:45:42,145 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
INFO 18:45:42,146 HaplotypeCaller - Disabling physical phasing, which is supported only for reference-model confidence output
INFO 18:45:42,180 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
WARN 18:45:42,181 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
INFO 18:45:42,181 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 18:45:42,251 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units

ERROR --
ERROR stack trace

java.lang.IllegalStateException: Rod span 1:1-249250621 isn't contained within the data shard 1:1-249250621, meaning we wouldn't get all of the data we need
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator.(TraverseActiveRegions.java:307)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:271)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
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 https://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Rod span 1:1-249250621 isn't contained within the data shard 1:1-249250621, meaning we wouldn't get all of the data we need
ERROR ------------------------------------------------------------------------------------------

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