Error converting files to SIF and BIOpax_level2

[kmgenoguin]

I got a fatal error exception shown at the bottom of the software when converting the systemic lupus erythematosus (SLE) pathway map into SIF and BIOpax_level2

[draeger]

The problem can be repoduced by running KEGGtranslator with the following options:

java -Duser.language=en -jar KEGGtranslator_v2.4.jar --gui=false -ihsa05322.xml -ohsa05322.sif -fSIF -rotrue --show-formula-for-compounds=true -nowhitetrue -artrue -noprtrue -mergetrue

Which will result in a NullPointerException

java.lang.NullPointerException
        at org.biopax.paxtools.impl.ModelImpl.add(ModelImpl.java:153)
        at org.biopax.paxtools.impl.ModelImpl.addNew(ModelImpl.java:132)
        at de.zbit.kegg.io.KEGG2BioPAX_level2.createPathwayInstance(Unknown Source)
        at de.zbit.kegg.io.KEGG2BioPAX.translateWithoutPreprocessing(Unknown Source)
        at de.zbit.kegg.io.KEGG2BioPAX.translateWithoutPreprocessing(Unknown Source)
        at de.zbit.kegg.io.AbstractKEGGtranslator.translate(Unknown Source)
        at de.zbit.kegg.io.AbstractKEGGtranslator.translate(Unknown Source)
        at de.zbit.kegg.io.AbstractKEGGtranslator.translate(Unknown Source)
        at de.zbit.kegg.Translator.translate(Unknown Source)
        at de.zbit.kegg.Translator.commandLineMode(Unknown Source)
        at de.zbit.Launcher.launchCommandLineMode(Unknown Source)
        at de.zbit.Launcher.run(Unknown Source)
        at de.zbit.Launcher.<init>(Unknown Source)
        at de.zbit.kegg.Translator.<init>(Unknown Source)
        at de.zbit.kegg.Translator.main(Unknown Source)