htsjdk.samtools.SAMException

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

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Solutions on the web6

  • via GitHub by PaolaD
    , 9 months ago
    Value was put into PairInfoMap more than once. 3073: SRR1517848.769506
  • Value was put into PairInfoMap more than once. 96: null:NB501257:32:HWCMVBGXX:1:21209:24100:6206
  • via GitHub by jjfarrell
    , 1 year ago
    Value was put into PairInfoMap more than once. 1: E00116:30:H0BL7ALXX:7:2202:27755:2311
  • Stack trace

    • htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 3073: SRR1517848.769506 at htsjdk.samtools.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:132) at htsjdk.samtools.CoordinateSortedPairInfoMap.access$300(CoordinateSortedPairInfoMap.java:53) at htsjdk.samtools.CoordinateSortedPairInfoMap$MapIterator.advanceToNextNonEmptyReferenceIndex(CoordinateSortedPairInfoMap.java:227) at htsjdk.samtools.CoordinateSortedPairInfoMap$MapIterator.<init>(CoordinateSortedPairInfoMap.java:221) at htsjdk.samtools.CoordinateSortedPairInfoMap$MapIterator.<init>(CoordinateSortedPairInfoMap.java:211) at htsjdk.samtools.CoordinateSortedPairInfoMap.iterator(CoordinateSortedPairInfoMap.java:208) at htsjdk.samtools.SamFileValidator$CoordinateSortedPairEndInfoMap.iterator(SamFileValidator.java:728) at htsjdk.samtools.SamFileValidator.validateUnmatchedPairs(SamFileValidator.java:227) at htsjdk.samtools.SamFileValidator.validateSamFile(SamFileValidator.java:200) at htsjdk.samtools.SamFileValidator.validateSamFileSummary(SamFileValidator.java:127) at picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:163) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

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