CalculateContamination error
A error occurred when use CalculateContamination, may I ask how to solve it
REQUIRED for all errors and issues:
a) GATK version used: GATK 4.4.0.0
b) Exact command used:
gatk --java-options "-Xmx100G -Djava.io.tmpdir=./" CalculateContamination \
-I pileups.table \
-O contamination.table
c) Entire program log:
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx100G -Djava.io.tmpdir=./ -jar /gatk4/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar CalculateContamination -I /pileups.table -O /contamination.table
13:32:38.073 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk4/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
13:32:38.167 INFO CalculateContamination - ------------------------------------------------------------
13:32:38.169 INFO CalculateContamination - The Genome Analysis Toolkit (GATK) v4.4.0.0
13:32:38.169 INFO CalculateContamination - For support and documentation go to https://software.broadinstitute.org/gatk/
13:32:38.169 INFO CalculateContamination - Executing as xxxxx@cu12 on Linux v3.10.0-862.el7.x86_64 amd64
13:32:38.170 INFO CalculateContamination - Java runtime: Java HotSpot(TM) 64-Bit Server VM v20.0.1+9-29
13:32:38.170 INFO CalculateContamination - Start Date/Time: July 10, 2023, 1:32:38<E2><80><AF>PM CST
13:32:38.170 INFO CalculateContamination - ------------------------------------------------------------
13:32:38.170 INFO CalculateContamination - ------------------------------------------------------------
13:32:38.175 INFO CalculateContamination - HTSJDK Version: 3.0.5
13:32:38.175 INFO CalculateContamination - Picard Version: 3.0.0
13:32:38.175 INFO CalculateContamination - Built for Spark Version: 3.3.1
13:32:38.176 INFO CalculateContamination - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:32:38.176 INFO CalculateContamination - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:32:38.176 INFO CalculateContamination - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:32:38.176 INFO CalculateContamination - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:32:38.176 INFO CalculateContamination - Deflater: IntelDeflater
13:32:38.176 INFO CalculateContamination - Inflater: IntelInflater
13:32:38.176 INFO CalculateContamination - GCS max retries/reopens: 20
13:32:38.176 INFO CalculateContamination - Requester pays: disabled
13:32:38.177 INFO CalculateContamination - Initializing engine
13:32:38.177 INFO CalculateContamination - Done initializing engine
13:33:57.562 INFO KernelSegmenter - Found 3 changepoints after applying the changepoint penalty.
13:33:59.552 INFO KernelSegmenter - Found 8 changepoints after applying the changepoint penalty.
13:34:01.786 INFO KernelSegmenter - Found 7 changepoints after applying the changepoint penalty.
13:34:03.536 INFO KernelSegmenter - Found 2 changepoints after applying the changepoint penalty.
13:34:05.434 INFO KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
13:34:07.617 INFO KernelSegmenter - Found 3 changepoints after applying the changepoint penalty.
13:34:09.241 INFO KernelSegmenter - Found 10 changepoints after applying the changepoint penalty.
13:34:11.116 INFO KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
13:34:12.863 INFO KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
13:34:13.924 INFO KernelSegmenter - Found 2 changepoints after applying the changepoint penalty.
13:34:17.606 INFO KernelSegmenter - Found 7 changepoints after applying the changepoint penalty.
13:34:20.400 INFO KernelSegmenter - Found 3 changepoints after applying the changepoint penalty.
13:34:23.722 INFO KernelSegmenter - Found 6 changepoints after applying the changepoint penalty.
13:34:26.535 INFO KernelSegmenter - Found 3 changepoints after applying the changepoint penalty.
13:34:29.199 INFO KernelSegmenter - Found 1 changepoints after applying the changepoint penalty.
13:34:32.342 INFO KernelSegmenter - Found 7 changepoints after applying the changepoint penalty.
13:34:34.492 INFO KernelSegmenter - Found 9 changepoints after applying the changepoint penalty.
13:34:42.359 INFO CalculateContamination - Shutting down engine
[July 10, 2023, 1:34:42?PM CST] org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination done. Elapsed time: 2.07 minutes.
Runtime.totalMemory()=56337891328
java.lang.IllegalArgumentException: log10p: Log10-probability must be 0 or less
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:798)
at org.broadinstitute.hellbender.utils.MathUtils.log10BinomialProbability(MathUtils.java:655)
at org.broadinstitute.hellbender.utils.MathUtils.binomialProbability(MathUtils.java:648)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.lambda$genotypeLikelihoods$18(ContaminationModel.java:267)
at org.broadinstitute.hellbender.utils.IndexRange.mapToDouble(IndexRange.java:171)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.genotypeLikelihoods(ContaminationModel.java:266)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.lambda$segmentLogLikelihood$19(ContaminationModel.java:280)
at java.base/java.util.stream.ReferencePipeline$6$1.accept(ReferencePipeline.java:248)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.DoublePipeline.collect(DoublePipeline.java:541)
at java.base/java.util.stream.DoublePipeline.sum(DoublePipeline.java:450)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.segmentLogLikelihood(ContaminationModel.java:280)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.lambda$calculateMinorAlleleFraction$15(ContaminationModel.java:235)
at org.apache.commons.math3.optim.univariate.UnivariateOptimizer.computeObjectiveValue(UnivariateOptimizer.java:149)
at org.apache.commons.math3.optim.univariate.BrentOptimizer.doOptimize(BrentOptimizer.java:139)
at org.apache.commons.math3.optim.univariate.BrentOptimizer.doOptimize(BrentOptimizer.java:43)
at org.apache.commons.math3.optim.BaseOptimizer.optimize(BaseOptimizer.java:153)
at org.apache.commons.math3.optim.univariate.UnivariateOptimizer.optimize(UnivariateOptimizer.java:70)
at org.broadinstitute.hellbender.utils.OptimizationUtils.max(OptimizationUtils.java:40)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.calculateMinorAlleleFraction(ContaminationModel.java:236)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.lambda$new$0(ContaminationModel.java:67)
at java.base/java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:104)
at java.base/java.util.stream.IntPipeline$Head.forEach(IntPipeline.java:617)
at org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.<init>(ContaminationModel.java:67)
at org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination.doWork(CalculateContamination.java:124)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
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yb87625 This looks like a possible bug. Could you share your pileups.table input file?
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