Re: [svtoolkit-help] "Invalid sequence position"

[John B. <jo...@we...>]

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...> 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 FAX: 287697