Java error "NoClassDefFoundError" when running PGDSpider on Mac Catalina
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Entering edit mode
17 months ago
bntjoanne ▴ 10

I wish to analyse SNP data in Bayescan. I'm trying to use PGDSpider to get the input files ready. I followed the instructions for downloading PGDSpider 2.1.1.5 on Mac as follows: (1). I updated Java. (2). I downloaded PGDSpider. (3). Then I tried java -Xmx1024m -Xms512m -jar PGDSpider2.jar in terminal, but got the following "NoClassDefFoundError" error:

jobentley@Setups-MacBook-Pro Downloads % cd PGDSpider_2.1.1.5
jobentley@Setups-MacBook-Pro PGDSpider_2.1.1.5 % java -Xmx1024m -Xms512m -jar PGDSpider2.jar
java.lang.NoClassDefFoundError: org/w3c/dom/ls/DocumentLS
    at java.base/java.lang.ClassLoader.defineClass1(Native Method)
    at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1017)
    at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:151)
    at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:821)
    at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:719)
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:642)
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:600)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
    at org.apache.xerces.jaxp.DocumentBuilderImpl.<init>(Unknown Source)
    at org.apache.xerces.jaxp.DocumentBuilderFactoryImpl.newDocumentBuilder(Unknown Source)
    at org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:861)
    at org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:773)
    at org.apache.log4j.xml.DOMConfigurator.configure(DOMConfigurator.java:901)
    at ch.unibe.iee.cmpg.pgdspider.PGDSpider.main(PGDSpider.java:17)
Caused by: java.lang.ClassNotFoundException: org.w3c.dom.ls.DocumentLS
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:602)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
    ... 15 more

Any ideas how to resolve this? Or, alternatively, alternative options for converting files into formats acceptable for Bayescan and Bayenv?

Mac PGDSpider Java SNP Catalina • 887 views
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1
Entering edit mode

In this case you may actually be using a too new version of java (if this thread is correct). Looks like you may need to use Java 7 or 8 (which will likely not run on catalina) based on PGDSpider manual page. You may have to find a different machine to do this.

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Entering edit mode

Ok, thanks. I have an older machine I can try.

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