Hi there, I recently started working on a project the uses BioJava 3.0.4 and am encountering a NoClassDefFound exception when I try to run it. This leads me to believe something is wrong with the classpath. However all the biojava jars are included. Has anyone had a similar problem or have any insight into where I should look next? Are there any other jars that biojava depends on other than the biojava jars from the downloads page. Any help would be greatly appreciated!
Here are the errors: Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358) at org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88) at org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118) at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86) at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:69) at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71) at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342) at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112) at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112) at org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105) at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53) at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation at java.util.concurrent.FutureTask.report(Unknown Source) at java.util.concurrent.FutureTask.get(Unknown Source) at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:289) at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:612) at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:180) at externalcalcs.BLASTRunner.writeBlast(BLASTRunner.java:143) at externalcalcs.Conservation.runConservation(Conservation.java:31) at externalcalcs.ExternalCalculations.runExternalCalcs(ExternalCalculations.java:58) at runtime.PACE.externalCalcs(PACE.java:298) at runtime.PACE.main(PACE.java:168) Thanks! Michael Noseworthy
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