I'm trying to use REALPHY to generate a phylogeny tree based on whole (bacterial) genomes. When I run the commands "REALPHY_V112 realphy_input realphy_output" or "java -jar RealPhy_v112.jar ~/Desktop/realphy_input ~/Desktop/realphy_output" I get the same error:
Exception in thread "main" 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:498) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58) Caused by: java.lang.ArrayIndexOutOfBoundsException: 1 at buildTreesFromSequenceData.RealPhy.readConfig(RealPhy.java:900) at buildTreesFromSequenceData.RealPhy.setVariables(RealPhy.java:853) at buildTreesFromSequenceData.RealPhy.<init>(RealPhy.java:195) at buildTreesFromSequenceData.RealPhy.main(RealPhy.java:70) ... 5 more
Not sure if it's due to the JAVA version or not...
