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  • GitHub comment 22#247979622
    via GitHub by hartleys
    ,
  • Issue with spike-ins
    via GitHub by 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. 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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