Re: [svtoolkit-help] Mismatched read pair insert sizes
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Re: [svtoolkit-help] Mismatched read pair insert sizes
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From: John B. <jo...@we...> - 2013-06-03 15:53:44
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Hi Bob,
Not sure what happened there - maybe I pasted in from 'less -S'. Anyway
here is the same error, hopefully intact.
Best,
John
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Mismatched read pair insert sizes for sample
4070 Normal: [ {WTCHG_33730:2:1101:10772:19659 113 22 20047976
23 100M = 20047705
271
CGCTATTTTGCTATTTTGCCGAGGCTGGTCTTGAGCTCCTGGGCTCAAGTGTGCCTCCTGCCCCAGCCTCCCGATGTGCTGGGATTATAGGAGTGAGCCA
##########################################################?:DB000)6<EED
=FC33BIIIIEC,2<2<??DDDDD:D??? RG:Z:WTCHG_33730 NM:i:0 SM:i:37
MQ:i:23 PQ:i:51 UQ:i:0 XQ:i:11}, {WTCHG_33730:2:1101:10772:19659 177
22 20047705 23 100M
= 20047976 271
TCCTAAAATTAAAAATAATTATCCAGGCGGGGTGGCGGGTGCCTGTAGTCCAAGCTACGTGGGAGTCTGAGACAGGAGAATGGCGTGAACCCGGGAGGTG
###################################################
#CB=GF?00?0:00**BF<FBC:*9:**1<2+A+HGC0F?8B2++A1++ RG:Z:WTCHG_33730
NM:i:2 SM:i:23 MQ:i:37 PQ:i:51 UQ:i:11 XQ:i:0} ]
at
org.broadinstitute.sv.discovery.ReadPairRecordFilter.checkReadPair(ReadPairRecordFilter.java:259)
at
org.broadinstitute.sv.discovery.ReadPairRecordFilter.generateReadPairs(ReadPairRecordFilter.java:212)
at
org.broadinstitute.sv.discovery.ReadPairRecordFilter.filterReadPairs(ReadPairRecordFilter.java:98)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.finishReadPairSelection(DeletionDiscoveryAlgorithm.java:231)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:180)
at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:110)
at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
at
org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at
org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:97)
at
org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:97)
at
org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at
org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at
org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:123)
at
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at
org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:77)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR
------------------------------------------------------------------------------------------
On Fri, May 31, 2013 at 5:11 PM, John Broxholme <jo...@we...> wrote:
> I'm seeing several of these during discovery (I run a single discovery
> command per chromosome - this is from 22), using version 1.04.1162:
>
> INFO 15:23:08,823 HelpFormatter - Program Args: -T SVDiscoveryWalker -R
> /users/johnb/SV/Genomes/hs37d5.fa -O
> /well/htseq/ILLUMINA-WGS/SV-Freeze5/OUTPUT-1162/d22/P0002.discovery.vcf
> -disableG
> ATKTraversal true -md
> /well/htseq/ILLUMINA-WGS/SV-Freeze5/OUTPUT-1162/metadata -configFile
> conf/hs37d5.conf -runDirectory
> /well/htseq/ILLUMINA-WGS/SV-Freeze5/OUTPUT-1162/d22 -genderMapFile /w
> ell/htseq/ILLUMINA-WGS/SV-Freeze5/OUTPUT-1162/gender.map -genomeMaskFile
> /users/johnb/SV/Genomes/hs37d5.mask.fa -partitionName P0002 -runFilePrefix
> P0002 -L 22:9990000-21010000 -searchLocus 2
> 2:10000000-19999999 -searchWindow 22:9990000-21010000 -searchMinimumSize
> 100 -searchMaximumSize 1000000
>
> ##### ERROR stack trace
> java.lang.RuntimeException: Mismatched read pair insert sizes for sample
> 4070 Normal: [ {WTCHG_33730:2:1101:10772:19659 113 22 20047976
> 23 100M = 20047705
> =FC33BIIIIEC,2<2<??DDDDD:D??? RG:Z:WTCHG_33730 NM:i:0 SM:i:37
> MQ:i:23 PQ:i:51 UQ:i:0 XQ:i:11}, {WTCHG_33730:2:1101:10772:19659 177
> 22 20047705 23 100M
> #CB=GF?00?0:00**BF<FBC:*9:**1<2+A+HGC0F?8B2++A1++ RG:Z:WTCHG_33730
> NM:i:2 SM:i:23 MQ:i:37 PQ:i:51 UQ:i:11 XQ:i:0} ]
> at
> org.broadinstitute.sv.discovery.ReadPairRecordFilter.checkReadPair(ReadPairRecordFilter.java:259)
> at
> org.broadinstitute.sv.discovery.ReadPairRecordFilter.generateReadPairs(ReadPairRecordFilter.java:212)
> at
> org.broadinstitute.sv.discovery.ReadPairRecordFilter.filterReadPairs(ReadPairRecordFilter.java:98)
> at
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.finishReadPairSelection(DeletionDiscoveryAlgorithm.java:231)
> at
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:180)
> at
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:110)
> at
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
> at
> org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
> at
> org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:97)
> at
> org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
> at
> org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
> at
> org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:123)
> at
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
> at
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
> at
> org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:77)
> at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
> ##### ERROR
> ------------------------------------------------------------------------------------------
>
> Any clues as to what's wrong?
> Thanks
> John
>
> --
> John Broxholme
> Wellcome Trust Centre for Human Genetics
> Roosevelt Drive, Oxford, OX3 7BN, UK
> Tel: (+44 1865) 287611 FAX: 287697
>
--
John Broxholme
Wellcome Trust Centre for Human Genetics
Roosevelt Drive, Oxford, OX3 7BN, UK
Tel: (+44 1865) 287611 FAX: 287697
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