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ERROR happened in BaseRecalibrator

I got the error in just one of my samples, all the others were done without any problems.
Could anyone help me to figure it out?

Thanks a lot.

INFO 10:44:23,885 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:44:23,888 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.4-7-g5e89f01, Compiled 2013/03/06 01:01:28
INFO 10:44:23,902 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 10:44:23,902 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 10:44:23,905 HelpFormatter - Program Args: -T BaseRecalibrator -I /home/hpc/paylong/yinhung_20130226/tmp/200-416/bwa/DE2459C/DE2459C.bwa.marked.realigned.fixed.bam -R /home/hpc/paylong/yinhung_20130226/references/ucsc.hg19.fasta -knownSites /home/hpc/paylong/yinhung_20130226/references/dbsnp_137.hg19.vcf -o /home/hpc/paylong/yinhung_20130226/tmp/200-416/bwa/DE2459C/DE2459C.bwa.marked.realigned.fixed.bam.recal_data.grp
INFO 10:44:23,906 HelpFormatter - Date/Time: 2013/04/11 10:44:23
INFO 10:44:23,906 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:44:23,906 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:44:23,951 ArgumentTypeDescriptor - Dynamically determined type of /home/hpc/paylong/yinhung_20130226/references/dbsnp_137.hg19.vcf to be VCF
INFO 10:44:24,031 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:44:24,239 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 10:44:24,246 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 10:44:24,277 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
INFO 10:44:24,309 RMDTrackBuilder - Loading Tribble index from disk for file /home/hpc/paylong/yinhung_20130226/references/dbsnp_137.hg19.vcf
INFO 10:44:24,730 GenomeAnalysisEngine - Creating shard strategy for 1 BAM files
INFO 10:44:24,734 GenomeAnalysisEngine - Done creating shard strategy
INFO 10:44:24,735 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 10:44:24,735 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 10:44:24,905 BaseRecalibrator - The covariates being used here:
INFO 10:44:24,906 BaseRecalibrator - ReadGroupCovariate
INFO 10:44:24,906 BaseRecalibrator - QualityScoreCovariate
INFO 10:44:24,906 BaseRecalibrator - ContextCovariate
INFO 10:44:24,906 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
INFO 10:44:24,906 BaseRecalibrator - CycleCovariate
INFO 10:44:24,919 ReadShardBalancer$1 - Loading BAM index data for next contig
INFO 10:44:24,919 ReadShardBalancer$1 - Done loading BAM index data for next contig
INFO 10:44:54,747 ProgressMeter - chr1:48598833 2.25e+04 30.0 s 22.3 m 1.5% 32.3 m 31.8 m
INFO 10:45:24,756 ProgressMeter - chr1:167951356 2.22e+05 60.0 s 4.5 m 5.4% 18.7 m 17.7 m
INFO 10:45:54,765 ProgressMeter - chr2:2762984 4.14e+05 90.0 s 3.6 m 8.0% 18.7 m 17.2 m
INFO 10:46:24,908 ProgressMeter - chr2:138119650 5.14e+05 120.0 s 3.9 m 12.3% 16.2 m 14.2 m
INFO 10:46:55,724 ProgressMeter - chr2:243153207 7.14e+05 2.5 m 3.5 m 15.7% 15.9 m 13.4 m

ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: START (100) > (99) STOP -- this should never happen -- call Mauricio!
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:537)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesRightTail(ReadClipper.java:193)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:389)
at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:392)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:244)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:131)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:230)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:218)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:109)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

Best Answer

Answers

  • I did use bwa aln to align the data. The version of it is 0.7.2. The problem was fixed after I added -rf BadCigar to the command line. I will use the latest version of BWA (0.7.3a) to realign and see if there are further problems. Thanks a lot.

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