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I need help. GATK Haplotypecaller says my dict is empty but it isn't??

carlshotwellcarlshotwell University of FloridaMember

The Error message I get is the following
INFO 12:25:14,659 HelpFormatter - ----------------------------------------------------------------------------------
INFO 12:25:14,662 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29
INFO 12:25:14,662 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 12:25:14,663 HelpFormatter - For support and documentation go to
INFO 12:25:14,663 HelpFormatter - [Thu Jan 12 12:25:14 EST 2017] Executing on Linux 2.6.32-573.26.1.el6.x86_64 amd64
INFO 12:25:14,663 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13 JdkDeflater
INFO 12:25:14,667 HelpFormatter - Program Args: -R /ufrc/ewang/carl.shotwell/maps/mm10/Mus_musculus/UCSC/mm10/Sequence/Chromosomes/mm10/hg19.fa -T HaplotypeCaller -I Control1_fixed.bam -stand_call_conf 10 -stand_emit_conf 10 -o Control1.raw.snps.indels.vcf
INFO 12:25:14,671 HelpFormatter - Executing as [email protected] on Linux 2.6.32-573.26.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13.
INFO 12:25:14,671 HelpFormatter - Date/Time: 2017/01/12 12:25:14
INFO 12:25:14,671 HelpFormatter - ----------------------------------------------------------------------------------
INFO 12:25:14,671 HelpFormatter - ----------------------------------------------------------------------------------
INFO 12:25:14,705 GenomeAnalysisEngine - Strictness is SILENT
INFO 12:25:14,853 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
INFO 12:25:14,860 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:25:14,998 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
INFO 12:25:15,061 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
INFO 12:25:15,064 GenomeAnalysisEngine - Reads file is unmapped. Skipping validation against reference.
INFO 12:25:15,166 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files

ERROR stack trace

java.lang.IllegalArgumentException: Dictionary cannot have size zero
at org.broadinstitute.gatk.utils.MRUCachingSAMSequenceDictionary.(
at org.broadinstitute.gatk.utils.GenomeLocParser$1.initialValue(
at org.broadinstitute.gatk.utils.GenomeLocParser$1.initialValue(
at java.lang.ThreadLocal.setInitialValue(
at java.lang.ThreadLocal.get(
at org.broadinstitute.gatk.utils.GenomeLocParser.getContigInfo(
at org.broadinstitute.gatk.utils.GenomeLocParser.getContigs(
at org.broadinstitute.gatk.utils.GenomeLocParser.(
at org.broadinstitute.gatk.utils.GenomeLocParser.(
at org.broadinstitute.gatk.utils.GenomeLocSortedSet.createSetFromSequenceDictionary(
at org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler.createOverMappedReads(
at org.broadinstitute.gatk.engine.datasources.reads.IntervalSharder.shardOverMappedReads(
at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.createShardIteratorOverMappedReads(
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getShardStrategy(
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.engine.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
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
ERROR MESSAGE: Dictionary cannot have size zero
ERROR ------------------------------------------------------------------------------------------

However, I have checked both the dict and the reference index, built them again manually, and they do not have a size of 0.
Here is my code
java -jar GenomeAnalysisTK.jar -R /ufrc/ewang/carl.shotwell/maps/mm10/Mus_musculus/UCSC/mm10/Sequence/Chromosomes/mm10/hg19.fa -T HaplotypeCaller -I Control1_fixed.bam -stand_call_conf 10 -stand_emit_conf 10 -o Control1.raw.snps.indels.vcf

Best Answer


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