Looks like a function a regression. I believe Jason Carey has a pull request
that fixes the regression. Thanks for reporting!
N
Thumb typed for added typos
> On Jan 27, 2015, at 10:48 AM, Ben Bimber <bbim...@gmail.com> wrote:
>
> FWIW, I see the same error on 1.127 as well.
>
> -Ben
>
>> On Tue, Jan 20, 2015 at 3:42 AM, Renan Valieris
>> <renan.valie...@cipe.accamargo.org.br> wrote:
>> bam is attached.
>>
>> command used:
>> java -jar picard-tools-1.128/picard.jar BuildBamIndex I=a.bam
>>
>> [Tue Jan 20 09:39:46 BRST 2015] picard.sam.BuildBamIndex INPUT=a.bam
>> VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5
>> MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
>> [Tue Jan 20 09:39:46 BRST 2015] Executing as user@machine on Linux
>> 3.13.0-36-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32; Picard
>> version: 1.128(c8e12338d226532b30e9ecdbf33180a073c3ffc7_1421081159)
>> IntelDeflater
>>
>>
>> Em 2015-01-20 01:21, Nils Homer escreveu:
>>> Can you send a file along with the command you used?
>>>
>>> N
>>>
>>> Thumb typed for added typos
>>>
>>>> On Jan 16, 2015, at 1:02 PM, Renan Valieris
>>>> <renan.valie...@cipe.accamargo.org.br> wrote:
>>>>
>>>> Hello,
>>>>
>>>> since version 1.127 I am getting the following exception thrown by
>>>> BuildBamIndex:
>>>>
>>>> Exception in thread "main" htsjdk.samtools.SAMException: Exception
>>>> creating BAM index for record XXXXX:00143:01038 131b aligned read.
>>>> at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:92)
>>>> at htsjdk.samtools.BAMIndexer.createIndex(BAMIndexer.java:291)
>>>> at htsjdk.samtools.BAMIndexer.createIndex(BAMIndexer.java:271)
>>>> at picard.sam.BuildBamIndex.doWork(BuildBamIndex.java:133)
>>>> at
>>>> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
>>>> at
>>>> picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
>>>> at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
>>>> Caused by: htsjdk.samtools.SAMException: BAM cannot be indexed without
>>>> setting a fileSource for record XXXXX:00143:01038 131b aligned read.
>>>> at
>>>> htsjdk.samtools.BAMIndexMetaData.recordMetaData(BAMIndexMetaData.java:130)
>>>> at
>>>> htsjdk.samtools.BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:182)
>>>> at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:90)
>>>> ... 6 more
>>>>
>>>> version 1.126 works fine and ValidateSamFile can't find anything wrong
>>>> with the bam.
>>>> I can send example files if necessary, even bam with a single read can
>>>> trigger the exception.
>>>>
>>>> Any idea on what is going on ?
>>>>
>>>>
>>>>
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>> New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
>> GigeNET is offering a free month of service with a new server in Ashburn.
>> Choose from 2 high performing configs, both with 100TB of bandwidth.
>> Higher redundancy.Lower latency.Increased capacity.Completely compliant.
>> http://p.sf.net/sfu/gigenet
>> _______________________________________________
>> Samtools-help mailing list
>> Samtools-help@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
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