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

GitHub | szilvajuhos | 11 months ago
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    GitHub comment 13#218425358

    GitHub | 11 months ago | szilvajuhos
    java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: 1

    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Cannot add sequence that already exists in SAMSequenceDictionary: 1

      at htsjdk.samtools.SAMSequenceDictionary.setSequences()
    2. HTS JDK
      SAMFileReader.<init>
      1. htsjdk.samtools.SAMSequenceDictionary.setSequences(SAMSequenceDictionary.java:68)
      2. htsjdk.samtools.SAMSequenceDictionary.<init>(SAMSequenceDictionary.java:45)
      3. htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:113)
      4. htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:502)
      5. htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:165)
      6. htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:124)
      7. htsjdk.samtools.SAMFileReader.init(SAMFileReader.java:689)
      8. htsjdk.samtools.SAMFileReader.<init>(SAMFileReader.java:201)
      9. htsjdk.samtools.SAMFileReader.<init>(SAMFileReader.java:156)
      9 frames
    3. picard.sam
      MarkDuplicates.doWork
      1. picard.sam.MarkDuplicates.openInputs(MarkDuplicates.java:355)
      2. picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:405)
      3. picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:177)
      3 frames
    4. picard.cmdline
      CommandLineProgram.instanceMain
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
      1 frame
    5. picard.sam
      MarkDuplicates.main
      1. picard.sam.MarkDuplicates.main(MarkDuplicates.java:161)
      1 frame