java.lang.Exception: ERROR ERROR ERROR: Reached end of bam file, there are 22763461 orphaned reads, which are marked as having a mapped pair, but no corresponding pair is found in the bam file. (Example Orphaned Read Name: D00118:263:C89KTANXX:4:1209:7544:95127)


Solutions on the web2

Solution icon of github
via GitHub by hartleys
, 1 year ago
ERROR ERROR ERROR: Reached end of bam file, there are 22763461 orphaned reads, which are marked as having a mapped pair, but no corresponding pair is found in the bam file. (Example Orphaned Read Name: D00118:263:C89KTANXX:4:1209:7544:95127)

Solution icon of github
via GitHub by royfrancis
, 1 year ago
ERROR ERROR ERROR: Reached end of bam file, there are 22763461 orphaned reads, which are marked as having a mapped pair, but no corresponding pair is found in the bam file. (Example Orphaned Read Name: D00118:263:C89KTANXX:4:1209:7544:95127)

Stack trace

java.lang.Exception: ERROR ERROR ERROR: Reached end of bam file, there are 22763461 orphaned reads, which are marked as having a mapped pair, but no corresponding pair is found in the bam file.
 (Example Orphaned Read Name: D00118:263:C89KTANXX:4:1209:7544:95127)
	at internalUtils.Reporter$.error(Reporter.scala:269)
	at internalUtils.commonSeqUtils$$anon$2.next(commonSeqUtils.scala:728)
	at internalUtils.commonSeqUtils$$anon$2.next(commonSeqUtils.scala:699)
	at internalUtils.stdUtils$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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