I get this when running aligner with a 6 minutes audio file. I got it working with an audio of 3 minutes length.
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
at edu.cmu.sphinx.linguist.aflat.AFlatLinguist.collectNextUnits(AFlatLin
guist.java:407)
at edu.cmu.sphinx.linguist.aflat.AFlatLinguist.collectNextUnits(AFlatLin
guist.java:413)
at edu.cmu.sphinx.linguist.aflat.AFlatLinguist.initUnitMaps(AFlatLinguis
t.java:362)
at edu.cmu.sphinx.linguist.aflat.AFlatLinguist.compileGrammar(AFlatLingu
ist.java:332)
at edu.cmu.sphinx.linguist.aflat.AFlatLinguist.allocate(AFlatLinguist.ja
va:266)
at edu.cmu.sphinx.decoder.search.AlignerSearchManager.allocate(AlignerSe
archManager.java:752)
at edu.cmu.sphinx.decoder.AbstractDecoder.allocate(AbstractDecoder.java:
87)
at edu.cmu.sphinx.recognizer.Recognizer.allocate(Recognizer.java:168)
at edu.cmu.sphinx.demo.aligner.Aligner.allocate(Aligner.java:240)
at edu.cmu.sphinx.demo.aligner.Aligner.align(Aligner.java:162)
at edu.cmu.sphinx.demo.aligner.AlignerDemo.main(AlignerDemo.java:58)
Long audio aligner is a bit outdated branch. I suggest you to use long audio aligner from trunk, it should work fairly well.