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

[Philine F. <p.f...@un...>]

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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