java.lang.OutOfMemoryError

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  • Out of memory in CombineGVCFs — GATK-Forum
    via by Unknown author,
  • output - Model Summary number_of_trees 500 model_size_in_bytes 281881559 min_depth 50 max_depth 50 mean_depth 50.0 min_leaves 44957 max_leaves 52239 mean_leaves 48751.7770 10-20 13:18:14.773 10.5.120.29:54321 13741 #56798-16 INFO: Method: GET , URI: /3/Models.java/DRF_model_R_1444752985632_30.java, route: /3/Models/(?<modelid>.*?)(\.java)?, parms: {model_id=DRF_model_R_1444752985632_30} 2015-10-20 13:18:44.418:WARN:oejs.ServletHandler:Error for /3/Models.java/DRF_model_R_1444752985632_30.java java.lang.OutOfMemoryError: Requested array size exceeds VM limit at java.util.Arrays.copyOf(Arrays.java:2367) at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130) at java.lang.StringBuilder.append(StringBuilder.java:143) at java.lang.StringBuilder.append(StringBuilder.java:183) at water.util.SB.p(SB.java:128) at hex.tree.TreeJCodeGen.generate(TreeJCodeGen.java:105) at hex.tree.SharedTreeModel.toJavaPredictBody(SharedTreeModel.java:231) at hex.Model.toJavaPredict(Model.java:1014) at hex.Model.toJava(Model.java:932) at hex.Model.toJava(Model.java:881) at water.api.ModelSchema.toJava(ModelSchema.java:126) at water.api.RequestServer.wrap(RequestServer.java:679) at water.api.RequestServer.serve(RequestServer.java:580) at water.JettyHTTPD$H2oDefaultServlet.doGeneric(JettyHTTPD.java:617) at water.JettyHTTPD$H2oDefaultServlet.doGet(JettyHTTPD.java:559) at javax.servlet.http.HttpServlet.service(HttpServlet.java:735) at javax.servlet.http.HttpServlet.service(HttpServlet.java:848) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135) at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:154) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116) at org.eclipse.jetty.server.Server.handle(Server.java:370) at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494) at org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:53)
    via by JM,
    • java.lang.OutOfMemoryError: Requested array size exceeds VM limit at java.util.Arrays.copyOf(Arrays.java:2367) at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130) at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114) at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:415) at java.lang.StringBuilder.append(StringBuilder.java:132) at htsjdk.variant.vcf.VCFEncoder.addGenotypeData(VCFEncoder.java:342) at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:145) at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:221) at org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:182) at org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:269) at org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.endPreviousStates(CombineGVCFs.java:269) at org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.reduce(CombineGVCFs.java:189) at org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.reduce(CombineGVCFs.java:110) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:291) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:280) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:279) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)

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