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)