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Old 05-18-2013, 07:35 PM   #1
jtackney
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Location: Utah

Join Date: May 2012
Posts: 16
Default picard-tools "Unrecognized tag type" error

I have an aligned, sorted, and indexed BAM file from a proton run following TMAP. I'm trying out picard-tools for the first time. I can't get anything to run without giving me the following error:

Exception in thread "main" net.sf.samtools.SAMFormatException: Unrecognized tag type: B
at net.sf.samtools.BinaryTagCodec.readValue(BinaryTagCodec.java:270)
at net.sf.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:220)
at net.sf.samtools.BAMRecord.decodeAttributes(BAMRecord.java:302)
at net.sf.samtools.BAMRecord.getAttribute(BAMRecord.java:282)
at net.sf.samtools.SAMRecord.isValid(SAMRecord.java:1438)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:468)
at net.sf.samtools.BAMFileReader$BAMFileIterator.<init>(BAMFileReader.java:433)
at net.sf.samtools.BAMFileReader$BAMFileIterator.<init>(BAMFileReader.java:423)
at net.sf.samtools.BAMFileReader.getIterator(BAMFileReader.java:226)
at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:305)
at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:37)
at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:109)
at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
at net.sf.picard.analysis.CollectInsertSizeMetrics.main(CollectInsertSizeMetrics.java:81)


I know a tag type of B is some sort of auxillary tag, but I don't know what it signifies and/or why picard doesn't like it.

Thanks for any direction...
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Old 05-18-2013, 11:07 PM   #2
BAMseek
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Location: St. Louis, MO, USA

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The B flag is an addition to the BAM/SAM specifications to support arrays of various types. Support for the B flag was added to Picard-Tools 1.51 (August 2011). Are you using an up-to-date version of Picard-Tools?
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Old 05-19-2013, 03:55 PM   #3
jtackney
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Ah, you were correct! Somehow I had installed 1.27, which looks quite different than the newer package of jar files. Thanks.
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