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[GATK 126.96.36.199] No non-zero singular values were found in creating a panel of normals for somatic CNV
I got an exception below in creating a PoN for somatic CNV on about 80 WGS samples. It consists of ~30 males and ~50 females. I was able to create PoNs successfully for each sex separately, but not all together. Sex chromosomes were excluded for the PoN creation for both sexes.
The exception message suggests to set
minimum-interval-median-percentile to a higher value. I wonder how higher it should be or what it means. Would you also help me understand the argument,
12:14:03.269 WARN HDF5SVDReadCountPanelOfNormals - Exception encountered during creation of panel of normals (org.broadinstitute.hellbender.exceptions.UserException: No non-zero singular values were found. It may be necessary to use stricter parameters for filtering. For example, use a larger value of minimum-interval-median-percentile.). Attempting to delete partial output in cromwell-executions/CNVSomaticPanelWorkflow/0c26e635-0641-4791-9769-adaa5cee0e87/call-CreateReadCountPanelOfNormals/execution/gatk_somatic_wgs.pon.hdf5... 18/02/18 12:14:03 INFO SparkUI: Stopped Spark web UI at http://192.168.1.12:4040 18/02/18 12:14:03 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped! 18/02/18 12:14:03 INFO MemoryStore: MemoryStore cleared 18/02/18 12:14:03 INFO BlockManager: BlockManager stopped 18/02/18 12:14:03 INFO BlockManagerMaster: BlockManagerMaster stopped 18/02/18 12:14:03 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped! 18/02/18 12:14:03 INFO SparkContext: Successfully stopped SparkContext 12:14:03.373 INFO CreateReadCountPanelOfNormals - Shutting down engine [February 18, 2018 12:14:03 PM CST] org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals done. Elapsed time: 3.64 minutes. Runtime.totalMemory()=16482041856 org.broadinstitute.hellbender.exceptions.GATKException: Could not create panel of normals. It may be necessary to use stricter parameters for filtering. For example, use a larger value of minimum-interval-median-percentile. at org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals.create(HDF5SVDReadCountPanelOfNormals.java:341) at org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals.runPipeline(CreateReadCountPanelOfNormals.java:269) at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:30) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:153) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195) at org.broadinstitute.hellbender.Main.main(Main.java:277) Caused by: org.broadinstitute.hellbender.exceptions.UserException: No non-zero singular values were found. It may be necessary to use stricter parameters for filtering. For example, use a larger value of minimum-interval-median-percentile. at org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals.create(HDF5SVDReadCountPanelOfNormals.java:317) ... 8 more