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Error of BaseRecalibrator, i have confirm all database and software are ok.
yuegeorge
hkMember ✭
INFO 12:31:08,666 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03
INFO 12:31:08,666 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 12:31:08,666 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 12:31:08,669 HelpFormatter - Program Args: -T BaseRecalibrator -R /media/Analysis/gatk_resource/ucsc.hg19.fasta -I aCGH5875.rmdup.bam -knownSites /media/Analysis/gatk_resource/dbsnp_138.hg19.vcf -knownSites /media/Analysis/gatk_resource/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -knownSites /media/Analysis/gatk_resource/1000G_phase1.indels.hg19.sites.vcf -o ./BaseRecal.grp
INFO 12:31:08,679 HelpFormatter -
INFO 12:31:08,679 HelpFormatter - Date/Time: 2014/11/14 12:31:08
INFO 12:31:08,679 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:31:08,679 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:31:09,102 GenomeAnalysisEngine - Strictness is SILENT
INFO 12:31:09,388 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 12:31:09,395 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:31:09,424 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
INFO 12:31:09,765 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 12:31:09,769 GenomeAnalysisEngine - Done preparing for traversal
INFO 12:31:09,769 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 12:31:09,770 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 12:31:09,770 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 12:31:09,881 BaseRecalibrator - The covariates being used here:
INFO 12:31:09,881 BaseRecalibrator - ReadGroupCovariate
INFO 12:31:09,881 BaseRecalibrator - QualityScoreCovariate
INFO 12:31:09,881 BaseRecalibrator - ContextCovariate
INFO 12:31:09,882 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
INFO 12:31:09,882 BaseRecalibrator - CycleCovariate
INFO 12:31:09,884 ReadShardBalancer$1 - Loading BAM index data
INFO 12:31:09,884 ReadShardBalancer$1 - Done loading BAM index data
INFO 12:31:13,174 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -25
at org.broadinstitute.gatk.utils.baq.BAQ.calcEpsilon(BAQ.java:185)
at org.broadinstitute.gatk.utils.baq.BAQ.hmm_glocal(BAQ.java:272)
at org.broadinstitute.gatk.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:553)
at org.broadinstitute.gatk.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:610)
at org.broadinstitute.gatk.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:536)
at org.broadinstitute.gatk.utils.baq.BAQ.baqRead(BAQ.java:680)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:481)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:257)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:130)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
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:107)
Answers
@yuegeorge
Hello,
This error usually means the program expects a list of things that is longer than the input. This may be an issue with read clips. Did you do any read trimming?
Thanks,
Sheila
@Sheila
Thanks Sheila,
Yes, i have filter low quality reads by our programme before analysis.
So how to solve this problem?
Many thanks.
@Sheila
If i use the same file to calling variants by HaplotypeCaller. Everything looks like fine. but once i run BaseRecalibrator, the erorr will happened.