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 ? > > > ------------------------------------------------------------------------------ > 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 ------------------------------------------------------------------------------ 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
