No JSON file produced

[imichalop]

Hi. I ran causal-cmd for an input file of 21273 continuous variables and 1000 samples on a 30 core machine with 300GB RAM, as follows:

java -Xmx290G -jar causal-cmd-1.1.3-jar-with-dependencies.jar --algorithm fges --data-type continuous --dataset 21273-1000.txt --delimiter tab --score sem-bic --out . --penaltyDiscount 10 --maxDegree -1 --json-graph --skip-latest --faithfulnessAssumed

While causal-cmd did successfully produce an fges_XXX.txt file, its corresponding JSON file (fges_XXX_graph.json) was empty, as it threw the following error messages:

Exception in thread "main" java.lang.IllegalArgumentException: NaN is not a valid double value as per JSON specification. To override this behavior, use GsonBuilder.serializeSpecialFloatingPointValues() method.                                                             
        at com.google.gson.Gson.checkValidFloatingPoint(Gson.java:324)                                                                                                                                                                                                         
        at com.google.gson.Gson$2.write(Gson.java:292)                                                                                                                                                                                                                         
        at com.google.gson.Gson$2.write(Gson.java:278)                                                                                                                                                                                                                         
        at com.google.gson.internal.bind.TypeAdapterRuntimeTypeWrapper.write(TypeAdapterRuntimeTypeWrapper.java:69)                                                                                                                                                            
        at com.google.gson.internal.bind.MapTypeAdapterFactory$Adapter.write(MapTypeAdapterFactory.java:208)                                                                                                                                                                   
        at com.google.gson.internal.bind.MapTypeAdapterFactory$Adapter.write(MapTypeAdapterFactory.java:145)                                                                                                                                                                   
        at com.google.gson.internal.bind.TypeAdapterRuntimeTypeWrapper.write(TypeAdapterRuntimeTypeWrapper.java:69)                                                                                                                                                            
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$1.write(ReflectiveTypeAdapterFactory.java:125)                                                                                                                                                           
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.write(ReflectiveTypeAdapterFactory.java:243)                                                                                                                                                     
        at com.google.gson.internal.bind.TypeAdapterRuntimeTypeWrapper.write(TypeAdapterRuntimeTypeWrapper.java:69)                                                                                                                                                            
        at com.google.gson.internal.bind.CollectionTypeAdapterFactory$Adapter.write(CollectionTypeAdapterFactory.java:97)                                                                                                                                                      
        at com.google.gson.internal.bind.CollectionTypeAdapterFactory$Adapter.write(CollectionTypeAdapterFactory.java:61)
        at com.google.gson.internal.bind.TypeAdapterRuntimeTypeWrapper.write(TypeAdapterRuntimeTypeWrapper.java:69)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$1.write(ReflectiveTypeAdapterFactory.java:125)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.write(ReflectiveTypeAdapterFactory.java:243)
        at com.google.gson.Gson.toJson(Gson.java:669)
        at com.google.gson.Gson.toJson(Gson.java:648)
        at com.google.gson.Gson.toJson(Gson.java:603)
        at com.google.gson.Gson.toJson(Gson.java:583)
        at edu.pitt.dbmi.causal.cmd.util.GraphIO.writeAsJSON(GraphIO.java:53)
        at edu.pitt.dbmi.causal.cmd.CausalCmdApplication.runTetrad(CausalCmdApplication.java:156)
        at edu.pitt.dbmi.causal.cmd.CausalCmdApplication.main(CausalCmdApplication.java:105)

What am I doing wrong? Best Regards, Ioannis

[kvb2univpitt]

@imichalop I apologize for the extremely late reply. I am going through the issues and realized I missed this one. Is it possible to share your fges_XXX.txt file?

[jdramsey]

This is s stale issue, cloisng.