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 cdemel@sa014 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)