Re: [svtoolkit-help] "Invalid sequence position"
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Re: [svtoolkit-help] "Invalid sequence position"
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From: Bob H. <han...@br...> - 2013-05-28 20:23:59
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This doesn't look like the entire stack trace. Did you truncate it? I'm happy to try to help, but you need to send me the full stack trace and you should send the full command line as well. -Bob On 5/28/13 10:37 AM, John Broxholme wrote: > Hi Bob, > > Thanks for the quick response.  Yes it is NCBI build37 (actually the > 1000G reference with decoy).  I can fill in a bit more detail on > this.  The error I sent earlier was using svtoolkit build 1.04.1068 > (which I couldn't use at first since dependency on some new(?) R > package required an upgrade of R).  I first saw this using our > production version, build 1.04.857: > > ... > INFO  11:41:09,579 ComputeGCProfiles - Opened reference GC profile. > INFO  11:41:09,579 ComputeGCProfiles - Processing input file > /gpfs1/well/htseq/ILLUMINA-WGS/SV-Freeze5/AS_CLL_156GL.bam ... > Exception in thread "main" java.lang.RuntimeException: Invalid > sequence position: 17:81195216 >     at > org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:40) >     at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) >     at > org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:23) >     at > org.broadinstitute.sv.apps.ComputeGCProfiles.main(ComputeGCProfiles.java:104) > Caused by: java.lang.IllegalArgumentException: Invalid sequence > position: 17:81195216 > ... > I note that the invalid coordinate reported differs - 81195216 > vs 81195230, although this is the same BAM. > > Anyhow, I have since updated picard-tools to 1.92 and run 'picard > validateSamFile on the offending BAM > The only error (in 10k errors) I see is "Mate not found for paired > read" (I see many of these) which I assume has been caused by deduping > (I used picard for this). > Meanwhile I have removed reads mapping to the last 100bp of chr17 from > that BAM, which is an ugly fix but it allows me to progress a bit. > And I have to resolve something else causing crashes with the current > (1.04.1068) version, which would be the subject of another thread... > > John > > On Thu, May 23, 2013 at 3:21 PM, John Broxholme <jo...@we... > <mailto:jo...@we...>> wrote: > > Pre-processing of one(of 270+) deep BAM files has failed with: > > ... > INFO  12:54:38,366 ComputeGCProfiles - Processing input file > org.broadinstitute.sv.dataset.SAMFileLocation@986cff74 ... > Exception in thread "main" java.lang.RuntimeException: Invalid > sequence position: 17:81195230 > ... > > Where would this have come from?  The pipeline has been the > same to prepare all 270+ of the (25x deep) BAMs, and this is the > only failure.  Any suggestions on what might be wrong and how to > fix it will be most welcome! > > Thanks > John > > -- > John Broxholme > Wellcome Trust Centre for Human Genetics > Roosevelt Drive, Oxford, OX3 7BN, UK > > > > > -- > John Broxholme > Wellcome Trust Centre for Human Genetics > Roosevelt Drive, Oxford, OX3 7BN, UK > Tel: (+44 1865) 287611 <tel:%28%2B44%201865%29%20287611> FAX: 287697 > > > ------------------------------------------------------------------------------ > Try New Relic Now & We'll Send You this Cool Shirt > New Relic is the only SaaS-based application performance monitoring service > that delivers powerful full stack analytics. Optimize and monitor your > browser, app, & servers with just a few lines of code. Try New Relic > and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
