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HaplotypeCaller Error

DemelDemel GöttingenMember

Hi,
when I try to run GATK HaplotypeCaller I always get the following error: > Non-monolithic file pointers must contain intervals from at most one contig
unfortunately, I could not find the source of the error. Here is the whole output:

INFO 17:52:36,254 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:52:36,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
INFO 17:52:36,256 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 17:52:36,256 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 17:52:36,259 HelpFormatter - Program Args: -T HaplotypeCaller -R /usr/users/cdemel/Annotation/human/hg20/GRCh38.spike.ins.no.patches.fa --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -I Jurkat_L_15min_1_AAGCCT_reheader.bam --sample_name Jurkat_L_15min_1_AAGCCT --genotyping_mode DISCOVERY -o /usr/users/cdemel/Analysis/RNAseq_final/SNPcalling/Jurkat_L_15min_1_AAGCCT.raw_variants.g.vcf.gz -nct 24 --unsafe ALL
INFO 17:52:36,264 HelpFormatter - Executing as [email protected] on Linux 3.10.0-229.14.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_85-mockbuild_2015_07_15_14_03-b00.
INFO 17:52:36,264 HelpFormatter - Date/Time: 2015/11/17 17:52:36
INFO 17:52:36,264 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:52:36,264 HelpFormatter - ---------------------------------------------------------------------------------
WARN 17:52:36,280 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values for --variant_index_type and --variant_index_parameter
WARN 17:52:36,282 GATKVCFUtils - Creating Tabix index for /usr/users/cdemel/Analysis/RNAseq_final/SNPcalling/Jurkat_L_15min_1_AAGCCT.raw_variants.g.vcf.gz, ignoring user-specified index type and parameter
INFO 17:52:36,359 GenomeAnalysisEngine - Strictness is SILENT
INFO 17:52:36,437 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
INFO 17:52:36,444 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 17:52:36,476 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
INFO 17:52:36,482 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
INFO 17:52:36,500 MicroScheduler - Running the GATK in parallel mode with 24 total threads, 24 CPU thread(s) for each of 1 data thread(s), of 24 processors available on this machine
INFO 17:52:36,556 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 17:52:36,560 GenomeAnalysisEngine - Done preparing for traversal
INFO 17:52:36,560 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 17:52:36,560 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 17:52:36,561 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
INFO 17:52:36,561 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
INFO 17:52:36,561 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
INFO 17:52:36,662 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
INFO 17:52:36,663 PairHMM - Performance profiling for PairHMM is disabled because HaplotypeCaller is being run with multiple threads (-nct>1) option
Profiling is enabled only when running in single thread mode

INFO 17:53:06,563 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s

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

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Non-monolithic file pointers must contain intervals from at most one contig
at org.broadinstitute.gatk.engine.datasources.reads.FilePointer.validateAllLocations(FilePointer.java:115)
at org.broadinstitute.gatk.engine.datasources.reads.FilePointer.(FilePointer.java:75)
at org.broadinstitute.gatk.engine.datasources.reads.FilePointer.(FilePointer.java:86)
at org.broadinstitute.gatk.engine.datasources.reads.FilePointer.union(FilePointer.java:393)
at org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancer.getCombinedFilePointersOnSingleContig(ActiveRegionShardBalancer.java:83)
at org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancer.access$000(ActiveRegionShardBalancer.java:40)
at org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancer$1.next(ActiveRegionShardBalancer.java:52)
at org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancer$1.next(ActiveRegionShardBalancer.java:46)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:90)
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: Non-monolithic file pointers must contain intervals from at most one contig
ERROR ------------------------------------------------------------------------------------------

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