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BDM-Lab / 3DMax

A maximum likelihood method for reconstructing 3D chromosome structure from chromosomal contact data
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Java issue #1

Closed MingleiYang closed 1 year ago

MingleiYang commented 2 years ago

Hi,

Thank you so much for developing this application, which helps us to understand the chromatin organisation better,

recently i tried to test this application and i came across this issue, which i think it related to my own Java setting. But i cannot figure out, could you please provide me some suggestions?

❯ java -jar 3DMax.jar parameters.txt
3DMax for Genome Structure.
INSTRUCTION:
 (1) Input the file containing the parameters.

Number of points: 57
Number of constraints: 1549
Max distance is: 40.475829797164664
Number of processors:1
Iteration 1, objective function:-252.13383, length of gradient 0.7558897
Iteration 2, objective function:-244.43569, length of gradient 0.7905352
Iteration 3, objective function:-238.78197, length of gradient 0.7799960
Iteration 4, objective function:-234.96316, length of gradient 0.7274894
Iteration 5, objective function:-232.30583, length of gradient 0.6571125
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Iteration 10, objective function:-224.14033, length of gradient 0.5161492
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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:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NoClassDefFoundError: org/apache/commons/math3/stat/correlation/SpearmansCorrelation
    at evaluation.Evaluate.calSpearmanCorrelation(Evaluate.java:257)
    at evaluation.CalRMSD.correlationIFvsDist(CalRMSD.java:141)
    at algorithm.StructureGenerator3DMax.run(StructureGenerator3DMax.java:480)
    at algorithm.StructureGenerator3DMax.generateStructure(StructureGenerator3DMax.java:411)
    at algorithm.StructureGenerator3DMax.main(StructureGenerator3DMax.java:769)
    ... 5 more
Caused by: java.lang.ClassNotFoundException: org.apache.commons.math3.stat.correlation.SpearmansCorrelation
    at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:445)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:587)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
    ... 10 more
yoeHuuui commented 2 years ago

I met the same problem some days ago, and then I install the openjdk-8-jdk. Now, I solved this problem. Maybe caused the version! More information you can clicked this link: https://stackoverflow.com/questions/59986900/exception-in-thread-main-java-lang-reflect-invocationtargetexception-while-ins