htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 3073: SRR1517848.769506

GitHub | PaolaD | 6 months ago
tip
Your exception is missing from the Samebug knowledge base.
Here are the best solutions we found on the Internet.
Click on the to mark the helpful solution and get rewards for you help.
  1. 0

    GitHub comment 77#254823316

    GitHub | 6 months ago | PaolaD
    htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 3073: SRR1517848.769506
  2. 0

    Exception running ValidateSam

    GitHub | 2 years ago | jjfarrell
    htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 1: E00116:30:H0BL7ALXX:7:2202:27755:2311

    Root Cause Analysis

    1. htsjdk.samtools.SAMException

      Value was put into PairInfoMap more than once. 3073: SRR1517848.769506

      at htsjdk.samtools.CoordinateSortedPairInfoMap.ensureSequenceLoaded()
    2. HTS JDK
      SamFileValidator.validateSamFileSummary
      1. htsjdk.samtools.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:132)
      2. htsjdk.samtools.CoordinateSortedPairInfoMap.access$300(CoordinateSortedPairInfoMap.java:53)
      3. htsjdk.samtools.CoordinateSortedPairInfoMap$MapIterator.advanceToNextNonEmptyReferenceIndex(CoordinateSortedPairInfoMap.java:227)
      4. htsjdk.samtools.CoordinateSortedPairInfoMap$MapIterator.<init>(CoordinateSortedPairInfoMap.java:221)
      5. htsjdk.samtools.CoordinateSortedPairInfoMap$MapIterator.<init>(CoordinateSortedPairInfoMap.java:211)
      6. htsjdk.samtools.CoordinateSortedPairInfoMap.iterator(CoordinateSortedPairInfoMap.java:208)
      7. htsjdk.samtools.SamFileValidator$CoordinateSortedPairEndInfoMap.iterator(SamFileValidator.java:728)
      8. htsjdk.samtools.SamFileValidator.validateUnmatchedPairs(SamFileValidator.java:227)
      9. htsjdk.samtools.SamFileValidator.validateSamFile(SamFileValidator.java:200)
      10. htsjdk.samtools.SamFileValidator.validateSamFileSummary(SamFileValidator.java:127)
      10 frames
    3. picard.sam
      ValidateSamFile.doWork
      1. picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:163)
      1 frame
    4. picard.cmdline
      PicardCommandLine.main
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
      2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
      3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
      3 frames