[Biojava-l] NoClassDefFoundError

[Mike Noseworthy]

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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