Opened 12 months ago
Closed 12 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: $<- -> $<-.data.frame Execution halted srun: error: cnl04: task 0: Exited with exit code 1 ...
Change History (4)
comment:1 by , 12 months ago
comment:3 by , 12 months ago
Resolution: | fixed |
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Status: | closed → reopened |
It seems like the fix in [7418] for creating a better message introduced a NullPointerException
.
java.lang.NullPointerException: Cannot invoke "java.lang.Float.floatValue()" because the return value of "net.sf.basedb.util.Values.getFloat(String, java.lang.Float)" is null at net.sf.basedb.reggie.grid.AscatJobCreator$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) ...
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In 7417: