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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via GitHub by hartleys
, 1 year 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
, 1 year 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.
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$$anon$4.next(stdUtils.scala:302)
at internalUtils.stdUtils$IteratorProgressReporter$$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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