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)
via GitHub by hartleys
, 1 week ago
FATAL ERROR: Cannot find chromosome "1" in genome FASTA file!
via GitHub by flissp
, 1 week ago
FATAL ERROR: Cannot find chromosome "1" in genome FASTA file!
via GitHub by royfrancis
, 1 week ago
ERROR ERROR ERROR: Reached end of bam file, there are 614946 orphaned reads, which are marked as having a mapped pair, but no corresponding pair is found in the bam file. (Example Orphaned Read Name: ST-E00215:230:HJ3FMALXX:2:1117:19096:15232)
via GitHub by royfrancis
, 1 week ago
FATAL ERROR: Cannot find chromosome "22" in genome FASTA file!
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)