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paxtools
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| ~% java -Xmx4g -jar paxtools-4.2.1.jar toSbgn 18.0/data/biopax-level2.owl l2.sbgn | |
| 4942 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 2.2 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction41985 property: DELTA-G) | |
| 4957 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 3.1 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction33853 property: DELTA-G) | |
| 4985 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 11.9 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction33446 property: DELTA-G) | |
| 4987 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 11.9 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction50368 property: DELTA-G) | |
| 5015 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: -3.4 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction43726 property: DELTA-G) | |
| 5016 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 5.7 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction45007 property: DELTA-G) | |
| 5017 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 1.5 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction65684 property: DELTA-G) | |
| 5018 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 1.1 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction64813 property: DELTA-G) | |
| 5018 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 0.4 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction44375 property: DELTA-G) | |
| 5043 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 0.4 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction42652 property: DELTA-G) | |
| 5116 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 7.1 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction58901 property: DELTA-G) | |
| 5117 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: -7.7 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction45938 property: DELTA-G) | |
| 5117 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 2. (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction33751 property: DELTA-G) | |
| 5117 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: -0.5 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction50559 property: DELTA-G) | |
| 5117 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: -5. (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction23478 property: DELTA-G) | |
| 5117 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: -7.2 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction27473 property: DELTA-G) | |
| 5118 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: -0.7 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction23058 property: DELTA-G) | |
| 5120 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: -8 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction24532 property: DELTA-G) | |
| 5121 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 0.5 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction64134 property: DELTA-G) | |
| 5237 [main] ERROR org.biopax.paxtools.io.BioPAXIOHandlerAdapter - Editor is null. This probably means an invalid BioPAX property. Failed to set 3.6.3.- | |
| 5267 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: -5 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction34035 property: DELTA-G) |
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| ~% java -Xmx4g -jar paxtools-4.2.1.jar toSif 18.0/data/biopax-level3.owl l3.sif | |
| 5352 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference115371 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference115371. null | |
| 5353 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference107862 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference107862. null | |
| 5353 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference84097 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference84097. null | |
| 5353 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference104062 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference104062. null | |
| 5353 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference104071 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference104071. null | |
| 5353 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference78078 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference78078. null | |
| 5353 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference87952 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference87952. null | |
| 5353 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference147872 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference147872. null | |
| 5855 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: NIL (element: http://biocyc.org/biopax/biopax-level3SmallMolecule130719 property: entityReference) | |
| 5955 [main] ERROR org.biopax.paxtools.io.BioPAXIOHandlerAdapter - Editor is null. This probably means an invalid BioPAX property. Failed to set 3.6.3.- | |
| Exception in thread "main" java.lang.IllegalArgumentException | |
| at org.biopax.paxtools.io.sif.level3.Group.addSubgroup(Group.java:82) | |
| at org.biopax.paxtools.io.sif.level3.Grouper.inferGroupFromComplex(Grouper.java:136) | |
| at org.biopax.paxtools.io.sif.level3.Grouper.inferGroups(Grouper.java:55) | |
| at org.biopax.paxtools.io.sif.level3.Grouper.inferGroups(Grouper.java:41) | |
| at org.biopax.paxtools.io.sif.level3.InteractionSetL3.<init>(InteractionSetL3.java:25) | |
| at org.biopax.paxtools.io.sif.SimpleInteractionConverter.inferL3(SimpleInteractionConverter.java:126) | |
| at org.biopax.paxtools.io.sif.SimpleInteractionConverter.inferInteractions(SimpleInteractionConverter.java:113) | |
| at org.biopax.paxtools.io.sif.SimpleInteractionConverter.writeInteractionsInSIF(SimpleInteractionConverter.java:354) | |
| at org.biopax.paxtools.PaxtoolsMain.toSif(PaxtoolsMain.java:308) | |
| at org.biopax.paxtools.PaxtoolsMain$Command$2.run(PaxtoolsMain.java:583) | |
| at org.biopax.paxtools.PaxtoolsMain.main(PaxtoolsMain.java:45) |
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