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 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.
via GitHub by hartleys
, 2 months ago
FATAL ERROR: Cannot find chromosome "1" in genome FASTA file!
via GitHub by flissp
, 2 months ago
FATAL ERROR: Cannot find chromosome "1" in genome FASTA file!
via GitHub by royfrancis
, 2 months 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
, 2 months ago
FATAL ERROR: Cannot find chromosome "22" in genome FASTA file!
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)