Hello, On Thu, Mar 24, 2016 at 12:40:05PM +0100, Gladbach wrote: > ERROR stack trace > > htsjdk.samtools.cram.CRAIIndex$CRAIIndexException: Expecting 6 columns > but got 1 > at htsjdk.samtools.cram.CRAIEntry.(CRAIEntry.java:51) > at htsjdk.samtools.cram.CRAIEntry.fromCraiLine(CRAIEntry.java:45) > at htsjdk.samtools.cram.CRAIIndex.readIndex(CRAIIndex.java:43) > at > htsjdk.samtools.cram.CRAIIndex.openCraiFileAsBaiStream(CRAIIndex.java:128) > at htsjdk.samtools.SamIndexes.asBaiSeekableStreamOrNull(SamIndexes.java:78) > at > org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.openIndexFile(GATKBAMIndex.java:314) > at
I don't know anything about GATK, but this stack trace implies it started off by opening GATKBAMINdex (I assume .bai) and somehow ended up in the CRAI (cram index) code, which then fails because it's not actually a cram index. I'm not a GATK developer or even user so I know very little about this, but it will help them if you can give the command line and file formats being used. What did you supply to GATK - BAM or CRAM? James -- James Bonfield ([email protected]) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
