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

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

Hi Bob,

sorry about my slow reply, we had some issues with our computing cluster. 

But now I managed to try out the latest interim release you suggested previously, unfortunately the error message stays the same (as you can see below). 
I also double checked that my input is a sorted bam. It was successfully run through realigning and recalibration using GATK, and SNPs and haplotypes can be called on this file utilizing GATK. 
Besides I also split the combined bam (paired end and mate pair libraries) into separate bams, which still gives the same error. 

Thanks for your help again, 
Philine 




##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.IllegalArgumentException: Left read of read pair fails left read test: HWI-ST143_0294:7:1:19426:37893#0       97      groupXXI        4523762 37
      46M     groupXXI        4529101 5385    CACTAAGTGCTTCCTCGATTTCGCCAAGATTTGTTCAGCATGGAAC  7767687877776676387776376787877768767777776886  X0:i:1  X1:i:0
  MD:Z:46 RG:Z:BS25pair   XG:i:0  AM:i:37 NM:i:0  SM:i:37 XM:i:0  XO:i:0  OQ:Z:IIIIIHIIIIEIIIIIHIIIIIIIIIGIHIIIIHIIGIGIIIBHII     XT:A:U
        at org.broadinstitute.sv.util.ReadPair.create(ReadPair.java:135)
        at org.broadinstitute.sv.discovery.ReadPairRecordFilter.createReadPair(ReadPairRecordFilter.java:300)
        at org.broadinstitute.sv.discovery.ReadPairRecordFilter.generateReadPairs(ReadPairRecordFilter.java:221)
        at org.broadinstitute.sv.discovery.ReadPairRecordFilter.filterReadPairs(ReadPairRecordFilter.java:97)
        at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.finishReadPairSelection(DeletionDiscoveryAlgorithm.java:216)
        at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:166)
        at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:165)
        at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:44)
        at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:85)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:236)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:116)
        at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
        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 1.0.5718M):
##### ERROR
##### ERROR Please visit the 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_0294:7:1:19426:37893#0      97      groupXXI        4523762 37      46M     groupXXI        4529101 5385    CACTAAGTGCTTCCTCGATTTCGCCAAGATTTGTTCAGCATGGAAC  7767687877776676387776376787877768767777776886  X0:i:1  X1:i:0  MD:Z:46 RG:Z:BS25pair   XG:i:0  AM:i:37 NM:i:0  SM:i:37 XM:i:0  XO:i:0  OQ:Z:IIIIIHIIIIEIIIIIHIIIIIIIIIGIHIIIIHIIGIGIIIBHII     XT:A:U
##### ERROR ------------------------------------------------------------------------------------------
    


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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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