Opened 7 years ago

Closed 7 years ago

#947 closed defect (fixed)

Demux fails if all barcodes have been used

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v4.9.2
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Stack trace: 

java.lang.NullPointerException 
  at net.sf.basedb.reggie.grid.DemuxJobCreator$DemuxJobCompletionHandler.parseDemultiplexMetrics(DemuxJobCreator.java:1077) 
  at net.sf.basedb.reggie.grid.DemuxJobCreator$DemuxJobCompletionHandler.jobCompleted(DemuxJobCreator.java:781) 
  at net.sf.basedb.reggie.grid.JobCompletionHandlerFactory$JobCompletionWrapper.jobCompleted(JobCompletionHandlerFactory.java:117) 
  at net.sf.basedb.opengrid.service.OpenGridService$JobCompletionInvoker.call(OpenGridService.java:847) 
  at net.sf.basedb.opengrid.service.OpenGridService.updateJobStatusInBase(OpenGridService.java:722) 
  at net.sf.basedb.opengrid.service.OpenGridService.processAsyncRequests(OpenGridService.java:519) 
  at net.sf.basedb.opengrid.service.OpenGridService$JobStatusTimerTask.run(OpenGridService.java:787) 
  at net.sf.basedb.util.timer.ThreadTimerTask$1.run(ThreadTimerTask.java:89) 
  at java.lang.Thread.run(Thread.java:745)

The NullPointerException happens because there are no reads registed to "UNUSED" barcodes.

Change History (1)

comment:1 by Nicklas Nordborg, 7 years ago

Resolution: → fixed
Status: new → closed

(In [4373]) Fixes #947: Demux fails if all barcodes have been used

If we don't get any reads the percentage mapped to unused barcode is set to 0.

A similar issue is also solved if the 'NNNN' entry is missing (but I think Picard may crash if it is not present so it should never happen).

Note: See TracTickets for help on using tickets.