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

GitHub | PaolaD | 1 month ago
  1. 0

    GitHub comment 77#254823316

    GitHub | 1 month ago | PaolaD
    htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 3073: SRR1517848.769506
  2. 0

    Exception running ValidateSam

    GitHub | 1 year ago | jjfarrell
    htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 1: E00116:30:H0BL7ALXX:7:2202:27755:2311
  3. 0

    Tophat v2.1.1 reports identical alignments and does not mark either as secondary.

    GitHub | 7 months ago | MatthewRalston
    htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 96: null:NB501257:32:HWCMVBGXX:1:21209:24100:6206
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  5. 0

    Hisat v2.0.1 reports identical alignments and does not mark either as secondary.

    GitHub | 7 months ago | MatthewRalston
    htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 3: null:NB501257:32:HWCMVBGXX:1:212$ 9:5229:14102
  6. 0

    CleanSam does not identify or remove duplicate alignments

    GitHub | 7 months ago | MatthewRalston
    htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 3: null:NB501257:32:HWCMVBGXX:1:21209:24100:6206

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    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