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

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

There isn't anything obviously wrong with that read.  There are a couple 
of things to try:
a) run Picard ValidateSamFile on the bam file to make sure it's ok
b) extract from the bam file both reads from the read pair so we can see 
both reads, for example:
samtools view in.bam | grep HWI-ST143_0294:7:1:19426:37893#0
c) create a small bam file containing just these two reads and see if 
the problem persists
(and if it does, send me the small bam file so I can debug).

-Bob

On 7/15/11 11:47 AM, Philine Feulner wrote:
> 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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