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

Google Groups | Richard | 8 months ago
  1. 0

    rnaseq error

    Google Groups | 8 months ago | Richard
    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
  2. 0

    ADAM build fails

    Google Groups | 3 years ago | Shyam Sarkar
    net.sf.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; Line 2 Line:
  3. 0

    GitHub comment 16#133070949

    GitHub | 1 year ago | drchriscole
    net.sf.samtools.SAMFormatException: SAM validation error: ERROR: Record 48757728, Read name HWI-ST1398:69:C26EMACXX:8:1101:1239:2242, Mapped mate should have mate reference name
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  5. 0

    GitHub comment 10#215742919

    GitHub | 7 months ago | AlexanderDilthey
    net.sf.samtools.SAMFormatException: SAM validation error: ERROR: Record 561917122, Read name ERR091571.55385293, MAPQ should be 0 for unmapped read.
  6. 0

    GitHub comment 10#215740129

    GitHub | 7 months ago | hgibling
    net.sf.samtools.SAMFormatException: SAM validation error: ERROR: Record 561917122, Read name ERR091571.55385293, MAPQ should be 0 for unmapped read.

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    Root Cause Analysis

    1. 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()
    2. picard
      SAMFileReader$AssertableIterator.next
      1. net.sf.samtools.SAMUtils.processValidationErrors(SAMUtils.java:448)
      2. net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:506)
      3. net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:487)
      4. net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:446)
      5. net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:641)
      6. net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:619)
      6 frames
    3. org.bioinfo.ngs
      NgsSmartMain.main
      1. org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.sortSamByName(ComputeCountsTask.java:142)
      2. org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.run(ComputeCountsTask.java:431)
      3. org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis.run(RNASeqQCAnalysis.java:68)
      4. org.bioinfo.ngs.qc.qualimap.main.RnaSeqQcTool.execute(RnaSeqQcTool.java:188)
      5. org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:187)
      6. org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111)
      6 frames