java.lang.RuntimeException

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    • java.lang.RuntimeException: invoke runExtractSpecies fails at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:873) at org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:768) at org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:749) at org.xmlcml.ami2.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:176) at org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:929) at org.xmlcml.ami2.plugins.species.SpeciesPlugin.main(SpeciesPlugin.java:36) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:871) ... 5 more Caused by: java.lang.NullPointerException at org.xmlcml.ami2.dictionary.DefaultAMIDictionary.contains(DefaultAMIDictionary.java:112) at org.xmlcml.ami2.plugins.AMISearcher.markFalsePositives(AMISearcher.java:380) at org.xmlcml.ami2.plugins.AMISearcher.search(AMISearcher.java:284) at org.xmlcml.ami2.plugins.AMIArgProcessor.searchSectionElements(AMIArgProcessor.java:298) at org.xmlcml.ami2.plugins.species.SpeciesArgProcessor.runExtractSpecies(SpeciesArgProcessor.java:57) ... 10 more
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