[ERROR] CreatePanelOfNormals

I am trying to use CreatePanelOfNormals for build a PoN.

java -Xmx128g -Djava.library.path=/usr/lib/jni/ -jar /root/gatk-protected.jar CreatePanelOfNormals -I /cromwell_root/fc-b9cc3b48-69c9-4013-8eba-ff7973fc7bc9/ee036d66-dddd-4176-a58b-cef52be2ec90/make_acnv_pon_workflow/ad221045-b616-4680-afa9-2d4c0b0bfa40/call-CombineReadCounts/BN10_TCGA_N__cnv_pon.merged.pcovs -O BN10_TCGA_N__cnv_pon.acnv.pon Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.Os5pIW

The .pcovs file includs 700+ samples.

however, I got the following ERROR:
[September 27, 2017 5:46:07 PM UTC] org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals done. Elapsed time: 10.89 minutes. Runtime.totalMemory()=74185703424 java.lang.NegativeArraySizeException at ncsa.hdf.hdf5lib.HDFArray.byteify(HDFArray.java:214) at ncsa.hdf.hdf5lib.H5.H5Dwrite(H5.java:2079) at org.broadinstitute.hellbender.utils.hdf5.HDF5File.writeDataset(HDF5File.java:950) at org.broadinstitute.hellbender.utils.hdf5.HDF5File.makeDataset(HDF5File.java:877) at org.broadinstitute.hellbender.utils.hdf5.HDF5File.makeDoubleMatrix(HDF5File.java:737) at org.broadinstitute.hellbender.utils.hdf5.HDF5PoN.setNormalCounts(HDF5PoN.java:412) at org.broadinstitute.hellbender.utils.hdf5.HDF5PoNCreator.writeTargetFactorNormalizeReadCountsAndTargetFactors(HDF5PoNCreator.java:159) at org.broadinstitute.hellbender.utils.hdf5.HDF5PoNCreator.createPoN(HDF5PoNCreator.java:99) at org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals.runPipeline(CreatePanelOfNormals.java:244) at org.broadinstitute.hellbender.utils.SparkToggleCommandLineProgram.doWork(SparkToggleCommandLineProgram.java:39) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:98) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:146) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:66) at org.broadinstitute.hellbender.Main.main(Main.java:81) 17/09/27 17:46:07 INFO ShutdownHookManager: Shutdown hook called 17/09/27 17:46:07 INFO ShutdownHookManager: Deleting directory /cromwell_root/tmp.Os5pIW/root/spark-fb9e0c4d-9c2f-4bf8-981f-8d796db06231 17/09/27 17:46:07 INFO RemoteActorRefProvider$RemotingTerminator: Shutting down remote daemon. 17/09/27 17:46:07 INFO RemoteActorRefProvider$RemotingTerminator: Remote daemon shut down; proceeding with flushing remote transports.

Thanks!

Best,
Chunyang

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by Sheila

Issue Number
2554
State
closed
Last Updated
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Closed By
chandrans

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