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ROBOT default memory 64G not enough? #254

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realmarcin opened this issue Sep 26, 2024 · 0 comments
Open

ROBOT default memory 64G not enough? #254

realmarcin opened this issue Sep 26, 2024 · 0 comments

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@realmarcin
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robot
remove -i /global/cfs/cdirs/m4689/master/kg-microbe/data/raw/ncbitaxon.owl --axioms "equivalent disjoint annotation abox type"
filter --exclude-terms /pscratch/sd/m/marcinj/kg-microbe/venv/lib/python3.10/site-packages/semsql/builder//exclude-terms.txt
-o /global/cfs/cdirs/m4689/master/kg-microbe/data/raw/ncbitaxon-min.owl

Picked up JAVA_TOOL_OPTIONS: -Xmx64G
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.base/java.util.Arrays.copyOf(Arrays.java:3720)
at java.base/java.util.Arrays.copyOf(Arrays.java:3689)
at java.base/java.util.ArrayList.toArray(ArrayList.java:401)
at java.base/java.util.ArrayList.(ArrayList.java:179)
at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.chooseAndSetOntologyIRI(OWLRDFConsumer.java:1430)
at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.endModel(OWLRDFConsumer.java:1393)
at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:152)
at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:71)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1303)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1243)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1200)
at org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:540)
at org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:425)
at org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:306)
at org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:483)
at org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:581)
at org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:539)
at org.obolibrary.robot.RemoveCommand.execute(RemoveCommand.java:117)
at org.obolibrary.robot.CommandManager.executeCommand(CommandManager.java:244)
at org.obolibrary.robot.CommandManager.execute(CommandManager.java:188)
at org.obolibrary.robot.CommandManager.main(CommandManager.java:135)
at org.obolibrary.robot.CommandLineInterface.main(CommandLineInterface.java:65)
make: *** [/pscratch/sd/m/marcinj/kg-microbe/venv/lib/python3.10/site-packages/semsql/builder/build.Makefile:43: /global/cfs/cdirs/m4689/master/kg-microbe/data/raw/ncbitaxon-min.owl] Error 1

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