java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: chr1

biostars.org | 6 months ago
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  1. 0

    error in samfile header

    biostars.org | 6 months ago
    java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: chr1

    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Cannot add sequence that already exists in SAMSequenceDictionary: chr1

      at net.sf.samtools.SAMSequenceDictionary.setSequences()
    2. picard
      CalculateHsMetrics.main
      1. net.sf.samtools.SAMSequenceDictionary.setSequences(SAMSequenceDictionary.java:62)
      2. net.sf.samtools.SAMSequenceDictionary.<init>(SAMSequenceDictionary.java:40)
      3. net.sf.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:106)
      4. net.sf.picard.util.IntervalList.fromReader(IntervalList.java:181)
      5. net.sf.picard.util.IntervalList.fromFile(IntervalList.java:152)
      6. net.sf.picard.analysis.directed.HsMetricsCalculator.<init>(HsMetricsCalculator.java:83)
      7. net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:83)
      8. net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
      9. net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:68)
      9 frames