[svtoolkit-help] Mismatched read pair insert sizes

[John B. <jo...@we...>]

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