Increase number of iterations in calculateContamination to 30 #6282
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I found a sample that fails when CalculateContamination is run.
The exception I get is:
org.apache.commons.math3.exception.TooManyEvaluationsException: illegal state: maximal count (20) exceeded: evaluations
at org.apache.commons.math3.optim.BaseOptimizer$MaxEvalCallback.trigger(BaseOptimizer.java:242)
at org.apache.commons.math3.util.Incrementor.incrementCount(Incrementor.java:155)
at org.apache.commons.math3.optim.BaseOptimizer.incrementEvaluationCount(BaseOptimizer.java:191)
at org.apache.commons.math3.optim.univariate.UnivariateOptimizer.computeObjectiveValue(UnivariateOptimizer.java:148)
at org.apache.commons.math3.optim.univariate.BrentOptimizer.doOptimize(BrentOptimizer.java:225)
at org.apache.commons.math3.optim.univariate.BrentOptimizer.doOptimize(BrentOptimizer.java:43)
at org.apache.commons.math3.optim.BaseOptimizer.optimize(BaseOptimizer.java:153)
at org.apache.commons.math3.optim.univariate.UnivariateOptimizer.optimize(UnivariateOptimizer.java:70)
at org.broadinstitute.hellbender.utils.OptimizationUtils.max(OptimizationUtils.java:40)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.lambda$calculateContamination$13(ContaminationModel.java:214)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.calculateContamination(ContaminationModel.java:215)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.(ContaminationModel.java:67)
at org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination.doWork(CalculateContamination.java:127)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
By increasing the maxEvaluations in calculateContamination from 20 to 30 this no longer throws an exception. Ideally I'd like to have a more principled way to decide on this upper bound.