java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: 1

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via GitHub by szilvajuhos
, 1 year ago
Cannot add sequence that already exists in SAMSequenceDictionary: 1
java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: 1
at htsjdk.samtools.SAMSequenceDictionary.setSequences(SAMSequenceDictionary.java:68)
at htsjdk.samtools.SAMSequenceDictionary.(SAMSequenceDictionary.java:45)
at htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:113)
at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:502)
at htsjdk.samtools.BAMFileReader.(BAMFileReader.java:165)
at htsjdk.samtools.BAMFileReader.(BAMFileReader.java:124)
at htsjdk.samtools.SAMFileReader.init(SAMFileReader.java:689)
at htsjdk.samtools.SAMFileReader.(SAMFileReader.java:201)
at htsjdk.samtools.SAMFileReader.(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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