java.lang.Exception: FATAL ERROR: SAMRecord is improperly paired! Is the file sorted by name? Offending reads: D00118:263:C89KTANXX:4:1101:1261:94887 != D00118:263:C89KTANXX:4:1101:1262:77904 If the file is not sorted by name then you should included the '--coordSorted' parameter. (Note: in coordSorted mode it is highly recommended but not actually required that the file be sorted by position) This problem could also have a number of other causes: if there are orphaned reads that aren't marked as such in the sam flags, for example.

GitHub | royfrancis | 5 months ago
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  1. 0

    Issue with spike-ins

    GitHub | 5 months ago | royfrancis
    java.lang.Exception: FATAL ERROR: SAMRecord is improperly paired! Is the file sorted by name? Offending reads: D00118:263:C89KTANXX:4:1101:1261:94887 != D00118:263:C89KTANXX:4:1101:1262:77904 If the file is not sorted by name then you should included the '--coordSorted' parameter. (Note: in coordSorted mode it is highly recommended but not actually required that the file be sorted by position) This problem could also have a number of other causes: if there are orphaned reads that aren't marked as such in the sam flags, for example.
  2. 0

    GitHub comment 22#247979622

    GitHub | 5 months ago | hartleys
    java.lang.Exception: FATAL ERROR: SAMRecord is improperly paired! Is the file sorted by name? Offending reads: D00118:263:C89KTANXX:4:1101:1261:94887 != D00118:263:C89KTANXX:4:1101:1262:77904 If the file is not sorted by name then you should included the '--coordSorted' parameter. (Note: in coordSorted mode it is highly recommended but not actually required that the file be sorted by position) This problem could also have a number of other causes: if there are orphaned reads that aren't marked as such in the sam flags, for example.

    Root Cause Analysis

    1. java.lang.Exception

      FATAL ERROR: SAMRecord is improperly paired! Is the file sorted by name? Offending reads: D00118:263:C89KTANXX:4:1101:1261:94887 != D00118:263:C89KTANXX:4:1101:1262:77904 If the file is not sorted by name then you should included the '--coordSorted' parameter. (Note: in coordSorted mode it is highly recommended but not actually required that the file be sorted by position) This problem could also have a number of other causes: if there are orphaned reads that aren't marked as such in the sam flags, for example.

      at internalUtils.Reporter$.error()
    2. internalUtils
      stdUtils$IteratorProgressReporter$$anon$4.next
      1. internalUtils.Reporter$.error(Reporter.scala:269)
      2. internalUtils.commonSeqUtils$$anon$1.next(commonSeqUtils.scala:682)
      3. internalUtils.commonSeqUtils$$anon$1.next(commonSeqUtils.scala:676)
      4. internalUtils.stdUtils$IteratorProgressReporter$$anon$4.next(stdUtils.scala:302)
      4 frames
    3. Scala
      Iterator$class.foreach
      1. scala.collection.Iterator$class.foreach(Iterator.scala:743)
      1 frame
    4. internalUtils
      stdUtils$IteratorProgressReporter$$anon$4.foreach
      1. internalUtils.stdUtils$IteratorProgressReporter$$anon$4.foreach(stdUtils.scala:296)
      1 frame
    5. qcUtils
      runAllQC$allQC_runner.run
      1. qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1055)
      2. qcUtils.runAllQC$.run(runAllQC.scala:774)
      3. qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:502)
      3 frames
    6. runner
      runner.main
      1. runner.runner$.main(runner.scala:92)
      2. runner.runner.main(runner.scala)
      2 frames