Re: [svtoolkit-help] Mismatched read pair insert sizes

[Bob H. <han...@br...>]

Your output below appears to be truncated or otherwised messed up (and 
note the strange characters too).
If you can send the exact output, probably we can figure out what's wrong.
Note that in particular the SEQ and TLEN fields are missing from these 
sam records.
-Bob

On 5/31/13 12:11 PM, John Broxholme 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 Â 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 1000000Â
>
> ##### ERROR stack traceÂ
> java.lang.RuntimeException: Mismatched read pair insert sizes for 
> sample 4070 Normal: [ {WTCHG_33730:2:1101:10772:19659 113 Â  Â  22 Â  
> Â Â 20047976 Â  Â  Â  Â 23 Â  Â  Â 100M Â  Â = Â  Â  Â 20047705
> =FC33BIIIIEC,2<2<??DDDDD:D??? Â  Â RG:Z:WTCHG_33730 Â  Â  Â  Â NM:i:0 
> Â SM:i:37 MQ:i:23 PQ:i:51 UQ:i:0 Â XQ:i:11}, 
> {WTCHG_33730:2:1101:10772:19659 Â  Â  Â  177 Â Â  22 Â  Â  Â 20047705 
> Â  Â  Â  Â 23 Â  Â  Â 100M
> #CB=GF?00?0:00**BF<FBC:*9:**1<2+A+HGC0F?8B2++A1++ Â  
> Â RG:Z:WTCHG_33730 Â  Â  Â  Â NM:i:2 Â SM:i:23 MQ:i:37 PQ:i:51 UQ:i:11 
> XQ:i:0} ]
> Â  Â  Â  Â  at 
> org.broadinstitute.sv.discovery.ReadPairRecordFilter.checkReadPair(ReadPairRecordFilter.java:259)
> Â  Â  Â  Â  at 
> org.broadinstitute.sv.discovery.ReadPairRecordFilter.generateReadPairs(ReadPairRecordFilter.java:212)
> Â  Â  Â  Â  at 
> org.broadinstitute.sv.discovery.ReadPairRecordFilter.filterReadPairs(ReadPairRecordFilter.java:98)
> Â  Â  Â  Â  at 
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.finishReadPairSelection(DeletionDiscoveryAlgorithm.java:231)
> Â  Â  Â  Â  at 
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:180)
> Â  Â  Â  Â  at 
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:110)
> Â  Â  Â  Â  at 
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
> Â  Â  Â  Â  at 
> org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
> Â  Â  Â  Â  at 
> org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:97)
> Â  Â  Â  Â  at 
> org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
> Â  Â  Â  Â  at 
> org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
> Â  Â  Â  Â  at 
> org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:123)
> Â  Â  Â  Â  at 
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
> Â  Â  Â  Â  at 
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
> Â  Â  Â  Â  at 
> org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:77)
> Â  Â  Â  Â  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
>
>
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