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)

Searched on Google with the first line of a JAVA stack trace?

We can recommend more relevant solutions and speed up debugging when you paste your entire stack trace with the exception message. Try a sample exception.

Recommended solutions based on your search

Solutions on the web

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)
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)
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$$anon$4.next(stdUtils.scala:302)
at internalUtils.stdUtils$IteratorProgressReporter$$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)

Users with the same issue

You are the first who have seen this exception.

Write tip

Know the solutions? Share your knowledge to help other developers to debug faster.