I am trying to run a mutation clustering algorithm described in

https://tinyheero.github.io/2015/08/26/TrAp.html

Running java -jar TrApWithDependencies.jar --text figure1.txt works fine on my laptop running windows 10, but not on AWS ubuntu. I would like to run it on my AWS instance because the algorithm is very RAM hungry and will run out of memory for input data with 50 or more rows.

Running it on Ubuntu Server 18.04 LTS gives me the following error. I believe the key issue is with Jama.Matrix

Exception in thread "main" java.lang.reflect.InvocationTargetException
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NoClassDefFoundError: Jama/Matrix
    at klugerlab.trap.data.Solution.fitClones(Solution.java:703)
    at klugerlab.trap.algo.MinimalClonesSolver.processTemplate(MinimalClonesSolver.java:168)
    at klugerlab.trap.algo.MinimalClonesSolver.completeSolutions(MinimalClonesSolver.java:204)
    at klugerlab.trap.algo.MinimalClonesSolver.runSolver(MinimalClonesSolver.java:250)
    at klugerlab.trap.algo.Solver.run(Solver.java:229)
    at klugerlab.trap.algo.Job.run(Job.java:97)
    at klugerlab.trap.TrApMain.main(TrApMain.java:120)
    ... 5 more
Caused by: java.lang.ClassNotFoundException: Jama.Matrix
    at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:471)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:588)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
    ... 12 more

I do not have access to the source code, only the .jar file.

0 Answers