Re: [svtoolkit-help] Left read of read pair fails left read test

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

I don't see any obvious problem with this SAM record.
Could you download the latest interim release from here:

ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/svtoolkit_1.04.683.tar.gz

and run with that.  This will produce a little bit of additional 
debugging information,
but mostly I'd like to see if the problem happens with more recent code.

-Bob

On 6/22/11 8:14 AM, Philine Feulner wrote:
> Hi,
>
> I am trying to run SVDiscovery on a non human data set (stickleback illumina paired end data).
> The installation test was successful and the bam files I am using are also already run through the GATK framework.
> The preprocessing of the reads also works but the SVDiscovery always fails with following error message:
> Left read of read pair fails left read test
> I attach the stack trace below.
>
> Sorry, I don't have any idea what this is suggesting and how to solve this issue.
>
> I would greatly appriciate any suggestions or help.
> Thanks in advance.
>
> Kind regards,
> Philine
>
>
>
>
>
> ##### ERROR stack trace
> java.lang.IllegalArgumentException: Left read of read pair fails left read test: HWI-ST143_0294:7:1:11533:163054#0      145     groupXXI        3556356 0       46M     groupXXI        3556505 104     TAATAGACGTACCGGGAGTTTAAGGGAGAGGTGCCACGGCTGTTAA  6776767466773666768867766676766777783677768677  X0:i:4  X1:i:2  XA:Z:scaffold_27,-2047944,46M,0;scaffold_27,-2047901,46M,0;scaffold_27,-2047858,46M,0;scaffold_108,+243775,46M,1;groupXX,+949641,46M,1; MD:Z:46 RG:Z:BS27pair.2 XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  MQ:i:0  OQ:Z:?DGDDGEGFGCIHHIIIIIHIBHIIIIIIIIIGIIHIIHIIIIHII     XT:A:R
>          at org.broadinstitute.sv.util.ReadPair.create(ReadPair.java:135)
>          at org.broadinstitute.sv.discovery.ReadPairRecordFilter.createReadPair(ReadPairRecordFilter.java:228)
>          at org.broadinstitute.sv.discovery.ReadPairRecordFilter.generateReadPairs(ReadPairRecordFilter.java:149)
>          at org.broadinstitute.sv.discovery.ReadPairRecordFilter.filterReadPairs(ReadPairRecordFilter.java:80)
>          at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.finishReadPairSelection(DeletionDiscoveryAlgorithm.java:206)
>          at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:156)
>          at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150)
>          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:75)
>          at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
>          at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
>          at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
>          at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
>          at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
>          at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
> ##### ERROR ------------------------------------------------------------------------------------------
> ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):
> ##### ERROR
> ##### ERROR Please visit to wiki to see if this is a known problem
> ##### ERROR If not, please post the error, with stack trace, to the GATK forum
> ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
> ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
> ##### ERROR
> ##### ERROR MESSAGE: Left read of read pair fails left read test: HWI-ST143_0294:7:1:11533:163054#0     145     groupXXI
>          3556356 0       46M     groupXXI        3556505 104     TAATAGACGTACCGGGAGTTTAAGGGAGAGGTGCCACGGCTGTTAA  6776767466773666768867766676766777783677768677  X0:i:4  X1:i:2  XA:Z:scaffold_27,-2047944,46M,0;scaffold_27,-2047901,46M,0;scaffold_27,-2047858,46M,0;scaffold_108,+243775,46M,1;groupXX,+949641,46M,1; MD:Z:46 RG:Z:BS27pair.2 XG:i:0  AM:i:0  NM:i:0  SM:i:0  XM:i:0  XO:i:0  MQ:i:0  OQ:Z:?DGDDGEGFGCIHHIIIIIHIBHIIIIIIIIIGIIHIIHIIIIHII     XT:A:R
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr Philine Feulner
> Westfälische Wilhelms University
> Institute for Evolution and Biodiversity
> Evolutionary Bioinformatics Group
> Hüfferstrasse 1
> 48149 Münster
> Germany
> Tel: +49 (0) 251 83 21636
> Fax: +49 (0) 251 83 24668
> Email: p.f...@un...
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
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