Complete this survey about your research needs and be entered to win an Amazon gift card or FireCloud credit.
Read more about it here!
Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.6 is out. See the GATK4 beta page for download and details.

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.

Sign In or Register to comment.