net.sf.samtools.SAMFormatException

SAM validation error: ERROR: Record 7, Read name ST-E00161:151:HKTTVCCXX:4:1101:10013:66830, Mapped mate should have mate reference name

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Solutions on the web21

  • via Google Groups by Richard, 6 months ago
    SAM validation error: ERROR: Record 7, Read name ST-E00161:151:HKTTVCCXX:4:1101:10013:66830, Mapped mate should have mate reference name
  • via GitHub by drchriscole
    , 1 year ago
    SAM validation error: ERROR: Record 48757728, Read name HWI-ST1398:69:C26EMACXX:8:1101:1239:2242, Mapped mate should have mate reference name
  • SAM validation error: ERROR: Record 109368398, Read name UNC11-SN627:380:C58DMACXX:5:1101:4427:2139, Mapped mate should have mate reference name
  • Stack trace

    • net.sf.samtools.SAMFormatException: SAM validation error: ERROR: Record 7, Read name ST-E00161:151:HKTTVCCXX:4:1101:10013:66830, Mapped mate should have mate reference name at net.sf.samtools.SAMUtils.processValidationErrors(SAMUtils.java:448) at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:506) at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:487) at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:446) at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:641) at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:619) at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.sortSamByName(ComputeCountsTask.java:142) at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.run(ComputeCountsTask.java:431) at org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis.run(RNASeqQCAnalysis.java:68) at org.bioinfo.ngs.qc.qualimap.main.RnaSeqQcTool.execute(RnaSeqQcTool.java:188) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:187) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111)

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