Opened 7 months ago

Closed 7 months ago

#1540 closed defect (fixed)

ASCAT fails when a solution can't be found

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.49.5
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

In the stacktrace we can find the following:

...
Warning message:
In runASCAT(lrr, baf, lrrsegm, bafsegm, ASCATobj$gender[arraynr],  :
  ASCAT could not find an optimal ploidy and purity value for sample S005117.l.d.a.lib.g.a.

Error in `$<-.data.frame`(`*tmp*`, normal_contamination, value = numeric(0)) : 
  replacement has 0 rows, data has 1
Calls: $<- -> $<-.data.frame
Execution halted
srun: error: cnl04: task 0: Exited with exit code 1
...

Change History (4)

comment:1 by Nicklas Nordborg, 7 months ago

In 7417:

References #1540: ASCAT fails when a solution can't be found

This fixes the crash in the R script. The job finishes with a message ASCAT analysis completed. Purity: ; Ploidy: ; Goodness of fit: which can be improved.

comment:2 by Nicklas Nordborg, 7 months ago

Resolution: fixed
Status: newclosed

In 7418:

Fixes #1540: ASCAT fails when a solution can't be found

Updated the message that is displayed when no solution was found to: ASCAT could not find an optimal ploidy and purity value.

The confirmation wizard will also display 'No solution' instead of an empty table.

comment:3 by Nicklas Nordborg, 7 months ago

Resolution: fixed
Status: closedreopened

It seems like the fix in [7418] for creating a better message introduced a NullPointerException.

java.lang.NullPointerException: Cannot invoke "java.lang.Float.floatValue()" because 
the return value of "net.sf.basedb.util.Values.getFloat(String, java.lang.Float)" is null
  at net.sf.basedb.reggie.grid.AscatJobCreator$AscatJobCompletionHandler.parseFiles(AscatJobCreator.java:397)
  at net.sf.basedb.reggie.grid.AscatJobCreator$AscatJobCompletionHandler.jobCompleted(AscatJobCreator.java:370)
  at net.sf.basedb.reggie.grid.JobCompletionHandlerFactory$JobCompletionWrapper.jobCompleted(JobCompletionHandlerFactory.java:196)
...

comment:4 by Nicklas Nordborg, 7 months ago

Resolution: fixed
Status: reopenedclosed

In 7430:

Fixes #1540: ASCAT fails when a solution can't be found

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