java.lang.IllegalArgumentException

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  • GitHub comment 13#218425358
    via GitHub by szilvajuhos
    ,
    • java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: 1 at htsjdk.samtools.SAMSequenceDictionary.setSequences(SAMSequenceDictionary.java:68) at htsjdk.samtools.SAMSequenceDictionary.<init>(SAMSequenceDictionary.java:45) at htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:113) at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:502) at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:165) at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:124) at htsjdk.samtools.SAMFileReader.init(SAMFileReader.java:689) at htsjdk.samtools.SAMFileReader.<init>(SAMFileReader.java:201) at htsjdk.samtools.SAMFileReader.<init>(SAMFileReader.java:156) at picard.sam.MarkDuplicates.openInputs(MarkDuplicates.java:355) at picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:405) at picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:177) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183) at picard.sam.MarkDuplicates.main(MarkDuplicates.java:161)
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