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 typosOn 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 moreversion 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
a.bam
Description: GNU Zip compressed data
------------------------------------------------------------------------------ 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
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