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.

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Solutions on the web6638

  • via GitHub by hartleys
    , 10 months ago
    '--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.
  • via GitHub by royfrancis
    , 9 months ago
    '--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.
  • via minecraftforge.net by Unknown author, 1 year ago
    <net.minecraftforge.fml.common(Mod.class[Mod, Javadoc: /**  * This defines a Mod to FML.  * Any class found with this annotation applied will be loaded as a Mod. The instance that is loaded will  * represent the mod to other Mods in the system. It will be sent various
  • Stack trace

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

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