[RESOLVIDO] Problemas em configurar log4j2 com mongodb

Bom dia, estou tentando configurar o log4j2 do meu projeto gradle para usar mongoDB, quando rodo o projeto dentro do eclipse ou rodo meus testes o log funciona sem problemas, porém quando gero o jar do projeto e rodo ele recebo o seguinte erro:

2018-08-13 09:30:11,534 main ERROR Unable to locate plugin type for MongoDb 2018-08-13 09:30:11,548 main ERROR Unable to locate plugin for MongoDb 2018-08-13 09:30:11,597 main ERROR Could not create plugin of type class org.apache.logging.log4j.core.appender.nosql.NoSqlAppender for element NoSql: java.lang.NullPointerException java.lang.NullPointerException at org.apache.logging.log4j.core.config.plugins.visitors.PluginElementVisitor.findNamedNode(PluginElementVisitor.java:103) 
    at org.apache.logging.log4j.core.config.plugins.visitors.PluginElementVisitor.visit(PluginElementVisitor.java:87) 
    at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.injectFields(PluginBuilder.java:181) 
    at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.build(PluginBuilder.java:122) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.createPluginObject(AbstractConfiguration.java:959) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:899) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:891) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.doConfigure(AbstractConfiguration.java:514) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.initialize(AbstractConfiguration.java:238) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.start(AbstractConfiguration.java:250) 
    at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:547) 
    at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:619) 
    at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:636) 
    at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:231) 
    at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:153) 
    at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:45) 
    at org.apache.logging.log4j.LogManager.getContext(LogManager.java:194) 
    at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:581) 
    at br.com.serversocket.main.Main.(Main.java:15)

2018-08-13 09:30:11,607 main ERROR Unable to invoke factory method in class org.apache.logging.log4j.core.appender.nosql.NoSqlAppender for element NoSql: java.lang.IllegalStateException: No factory method found for class org.apache.logging.log4j.core.appender.nosql.NoSqlAppender java.lang.IllegalStateException: No factory method found for class org.apache.logging.log4j.core.appender.nosql.NoSqlAppender 
    at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.findFactoryMethod(PluginBuilder.java:235) 
    at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.build(PluginBuilder.java:135) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.createPluginObject(AbstractConfiguration.java:959) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:899) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:891) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.doConfigure(AbstractConfiguration.java:514) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.initialize(AbstractConfiguration.java:238) 
    at org.apache.logging.log4j.core.config.AbstractConfiguration.start(AbstractConfiguration.java:250) 
    at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:547) 
    at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:619) 
    at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:636) 
    at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:231) 
    at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:153) 
    at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:45) 
    at org.apache.logging.log4j.LogManager.getContext(LogManager.java:194) 
    at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:581) 
    at br.com.serversocket.main.Main.(Main.java:15)

2018-08-13 09:30:11,617 main ERROR Null object returned for NoSql in appenders. 2018-08-13 09:30:11,655 main ERROR Unable to locate appender "NoSql" for logger config "root"

segue minhas configurações:

log4j2.yaml:

Configuration:
  status: WARN
  appenders:    
    NoSql:
      name: NoSql
      MongoDb:
        databaseName: tracker
        collectionName: appLog
        server: ds261755.mlab.com
        port: 61755
        username: admin
        password: XXXXX
  Loggers:
    logger:
      -
        name: com.memorynotfound
        level: info
      -
        name: com.mchange.v2.c3p0
        level: warn
    Root:
      level: info
      AppenderRef:
        ref: NoSql

build.gradle:

apply plugin: 'java'
apply plugin: 'application'
apply plugin: 'eclipse'
archivesBaseName = 'ServerSocket'
version = '3.2.1'

mainClassName = 'br.com.serversocket.main.Main'

compileTestJava {
 	sourceCompatibility = 1.8
	targetCompatibility = 1.8
}

compileJava {
	sourceCompatibility = 1.7
	targetCompatibility = 1.7
}

jar {
    dependsOn 'test'
    archiveName = "ServerSocket.jar"
	from {
		configurations.runtime.collect {
			it.isDirectory() ? it : zipTree(it)
		}

        configurations.compile.collect {
            it.isDirectory() ? it : zipTree(it)
        }
    }

    manifest {
        attributes 'Main-Class': 'br.com.serversocket.main.Main'
    }

    exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA'
}

test{
	useJUnitPlatform()
	dependsOn 'cleanTest'

    testLogging {
        events "passed", "skipped", "failed"
    }
    afterTest { desc, result -> 
        logger.quiet "Executing test ${desc.name} [${desc.className}] with result: ${result.resultType}"
    }
    testLogging {
        exceptionFormat = 'full'
    }	
}

eclipse.classpath.file.whenMerged {
  entries.each { println it.path }
}
configurations { 
	providedCompile 
}

repositories {
    mavenCentral()
    mavenLocal()
}

ext {
	jacksonVersion = '2.9.1'
	hibernateVerison = '5.1.0.Final'
	slf4jVerison = '1.7.25'
	log4jVerison = '2.11.1'
	junitVersion = '5.2.0'
	emailVersion = '1.6.1'
}

dependencies {
	
	//compile files(fileTree(dir: 'lib', includes: ['*.jar']))	
	compile "org.hibernate:hibernate-jpamodelgen:${hibernateVerison}"
	compile "org.hibernate:hibernate-c3p0:${hibernateVerison}"
	compile "org.hibernate:hibernate-core:${hibernateVerison}"
	compile "org.hibernate:hibernate-entitymanager:${hibernateVerison}"
	
	compile "org.slf4j:slf4j-simple:${slf4jVerison}"
	compile "org.slf4j:slf4j-api:${slf4jVerison}"
	
	compile "org.apache.logging.log4j:log4j-slf4j-impl:${log4jVerison}"
	compile "org.apache.logging.log4j:log4j-api:${log4jVerison}"
	compile "org.apache.logging.log4j:log4j-core:${log4jVerison}"
	compile "org.apache.logging.log4j:log4j-nosql:2.9.1"
	compile "org.apache.logging.log4j:log4j-jcl:${log4jVerison}"
	
	
	compile "com.fasterxml.jackson.core:jackson-core:${jacksonVersion}"
	compile "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}"
	compile "com.fasterxml.jackson.core:jackson-annotations:${jacksonVersion}"
	compile "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:${jacksonVersion}"
	
	compile "javax.mail:javax.mail-api:${emailVersion}"
	compile "com.sun.mail:javax.mail:${emailVersion}"
	
	compile group: 'org.projectlombok', name: 'lombok', version: '1.18.2'
	compile group: 'org.yaml', name: 'snakeyaml', version: '1.21'

	compile group: 'mysql', name: 'mysql-connector-java', version: '5.1.44'
	compile group: 'org.hibernate.common', name: 'hibernate-commons-annotations', version: '5.0.1.Final'
	compile group: 'org.hibernate.javax.persistence', name: 'hibernate-jpa-2.1-api', version: '1.0.2.Final'
	compile group: 'com.mchange', name: 'c3p0', version: '0.9.2.1'
	compile group: 'org.eclipse.persistence', name: 'javax.persistence', version: '2.1.0'
	compile group: 'org.jboss.logging', name: 'jboss-logging', version: '3.3.1.Final'
	compile group: 'commons-logging', name: 'commons-logging', version: '1.0.3'
	compile group: 'org.apache.mina', name: 'mina-core', version: '2.0.19'
	compile group: 'antlr', name: 'antlr', version: '2.7.7'
	compile group: 'com.fasterxml', name: 'classmate', version: '1.3.0'
	compile group: 'commons-codec', name: 'commons-codec', version: '1.11'
	compile group: 'commons-beanutils', name: 'commons-beanutils', version: '1.6'
	compile group: 'commons-collections', name: 'commons-collections', version: '3.2.1'
	compile group: 'org.apache.commons', name: 'commons-email', version: '1.5'
	compile group: 'commons-httpclient', name: 'commons-httpclient', version: '3.1'
	compile group: 'commons-lang', name: 'commons-lang', version: '2.3'
	compile group: 'commons-discovery', name: 'commons-discovery', version: '0.2'
	compile group: 'dom4j', name: 'dom4j', version: '1.6.1'
	compile group: 'net.sf.ehcache', name: 'ehcache', version: '1.5.0'
	compile group: 'org.apache.geronimo.specs', name: 'geronimo-jta_1.1_spec', version: '1.1.1'
	compile group: 'org.jboss', name: 'jandex', version: '2.0.3.Final'
	compile group: 'org.javassist', name: 'javassist', version: '3.22.0-GA'
	compile group: 'jdom', name: 'jdom', version: '1.1'
	compile group: 'javax.transaction', name: 'jta', version: '1.1'
	compile group: 'com.vividsolutions', name: 'jts', version: '1.13'
	compile group: 'org.apache.axis', name: 'axis', version: '1.4'
	compile group: 'axis', name: 'axis-jaxrpc', version: '1.4'
	compile group: 'javax.xml.soap', name: 'saaj-api', version: '1.3'
	compile group: 'wsdl4j', name: 'wsdl4j', version: '1.6.2'
	compile group: 'com.mchange', name: 'mchange-commons-java', version: '0.2.3.4'
	compile group: 'org.mongodb', name: 'mongo-java-driver', version: '3.8.0'


	testCompile group: 'com.h2database', name: 'h2', version: '1.4.197'
	testCompile "org.junit.jupiter:junit-jupiter-api:${junitVersion}"
	testCompile "org.junit.jupiter:junit-jupiter-engine:${junitVersion}"
	testCompile "org.junit.jupiter:junit-jupiter-params:${junitVersion}"
	testCompile group: 'org.junit.platform', name: 'junit-platform-launcher', version: '1.2.0'
}

configurations {
    all*.exclude group: 'javassist', module: 'javassist'
}

investiguei melhor o problema e está me parecendo algum problema no empacotamento das dependencias, fiz algumas alterações de configuração:

build.gradle:

apply plugin: 'java'
apply plugin: 'application'
apply plugin: 'eclipse'
archivesBaseName = 'ServerSocket'
version = '3.2.1'

mainClassName = 'br.com.serversocket.main.Main'

compileTestJava {
 	sourceCompatibility = 1.8
	targetCompatibility = 1.8
}

compileJava {
	sourceCompatibility = 1.7
	targetCompatibility = 1.7
}

jar {
    //dependsOn 'test'
    archiveName = "ServerSocket.jar"
	from {
		configurations.runtime.collect {
			it.isDirectory() ? it : zipTree(it)
		}

        configurations.compile.collect {
            it.isDirectory() ? it : zipTree(it)
        }
    }

    manifest {
        attributes 'Main-Class': 'br.com.serversocket.main.Main'
    }

    exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA'
}

test{
	useJUnitPlatform()
	dependsOn 'cleanTest'

    testLogging {
        events "passed", "skipped", "failed"
    }
    afterTest { desc, result -> 
        logger.quiet "Executing test ${desc.name} [${desc.className}] with result: ${result.resultType}"
    }
    testLogging {
        exceptionFormat = 'full'
    }	
}

eclipse.classpath.file.whenMerged {
  entries.each { println it.path }
}
configurations { 
	providedCompile 
}

repositories {
    mavenCentral()
    mavenLocal()
}

ext {
	jacksonVersion = '2.9.1'
	hibernateVerison = '5.1.0.Final'
	slf4jVerison = '1.7.25'
	log4jVerison = '2.11.1'
	junitVersion = '5.2.0'
	emailVersion = '1.6.1'
	mongoDBVersion = '3.8.0'
}

dependencies {
	
	//compile files(fileTree(dir: 'lib', includes: ['*.jar']))	
	compile "org.hibernate:hibernate-jpamodelgen:${hibernateVerison}"
	compile "org.hibernate:hibernate-c3p0:${hibernateVerison}"
	compile "org.hibernate:hibernate-core:${hibernateVerison}"
	compile "org.hibernate:hibernate-entitymanager:${hibernateVerison}"
	
	compile "org.slf4j:slf4j-simple:${slf4jVerison}"
	compile "org.slf4j:slf4j-api:${slf4jVerison}"
	
	compile "org.apache.logging.log4j:log4j-api:${log4jVerison}"
	compile "org.apache.logging.log4j:log4j-core:${log4jVerison}"
	compile "org.apache.logging.log4j:log4j-jcl:${log4jVerison}"
	compile "org.apache.logging.log4j:log4j-mongodb3:${log4jVerison}"
	//compile "org.apache.logging.log4j:log4j-nosql:${log4jVerison}"
	
	compile "com.fasterxml.jackson.core:jackson-core:${jacksonVersion}"
	compile "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}"
	compile "com.fasterxml.jackson.core:jackson-annotations:${jacksonVersion}"
	compile "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:${jacksonVersion}"
	
	compile "javax.mail:javax.mail-api:${emailVersion}"
	compile "com.sun.mail:javax.mail:${emailVersion}"
	
	//compile "org.mongodb:mongo-java-driver:${mongoDBVersion}"
	compile "org.mongodb:mongodb-driver:${mongoDBVersion}"
	compile "org.mongodb:mongodb-driver-core:${mongoDBVersion}"
	compile "org.mongodb:bson:${mongoDBVersion}"
	
	
	compile group: 'org.projectlombok', name: 'lombok', version: '1.18.2'
	compile group: 'org.yaml', name: 'snakeyaml', version: '1.21'

	compile group: 'mysql', name: 'mysql-connector-java', version: '5.1.44'
	compile group: 'org.hibernate.common', name: 'hibernate-commons-annotations', version: '5.0.1.Final'
	compile group: 'org.hibernate.javax.persistence', name: 'hibernate-jpa-2.1-api', version: '1.0.2.Final'
	compile group: 'com.mchange', name: 'c3p0', version: '0.9.2.1'
	compile group: 'org.eclipse.persistence', name: 'javax.persistence', version: '2.1.0'
	compile group: 'org.jboss.logging', name: 'jboss-logging', version: '3.3.1.Final'
	compile group: 'commons-logging', name: 'commons-logging', version: '1.0.3'
	compile group: 'org.apache.mina', name: 'mina-core', version: '2.0.19'
	compile group: 'antlr', name: 'antlr', version: '2.7.7'
	compile group: 'com.fasterxml', name: 'classmate', version: '1.3.0'
	compile group: 'commons-codec', name: 'commons-codec', version: '1.11'
	compile group: 'commons-beanutils', name: 'commons-beanutils', version: '1.6'
	compile group: 'commons-collections', name: 'commons-collections', version: '3.2.1'
	compile group: 'org.apache.commons', name: 'commons-email', version: '1.5'
	compile group: 'commons-httpclient', name: 'commons-httpclient', version: '3.1'
	compile group: 'commons-lang', name: 'commons-lang', version: '2.3'
	compile group: 'commons-discovery', name: 'commons-discovery', version: '0.2'
	compile group: 'dom4j', name: 'dom4j', version: '1.6.1'
	compile group: 'net.sf.ehcache', name: 'ehcache', version: '1.5.0'
	compile group: 'org.apache.geronimo.specs', name: 'geronimo-jta_1.1_spec', version: '1.1.1'
	compile group: 'org.jboss', name: 'jandex', version: '2.0.3.Final'
	compile group: 'org.javassist', name: 'javassist', version: '3.22.0-GA'
	compile group: 'jdom', name: 'jdom', version: '1.1'
	compile group: 'javax.transaction', name: 'jta', version: '1.1'
	compile group: 'com.vividsolutions', name: 'jts', version: '1.13'
	compile group: 'org.apache.axis', name: 'axis', version: '1.4'
	compile group: 'axis', name: 'axis-jaxrpc', version: '1.4'
	compile group: 'javax.xml.soap', name: 'saaj-api', version: '1.3'
	compile group: 'wsdl4j', name: 'wsdl4j', version: '1.6.2'
	compile group: 'com.mchange', name: 'mchange-commons-java', version: '0.2.3.4'


	testCompile group: 'com.h2database', name: 'h2', version: '1.4.197'
	testCompile "org.junit.jupiter:junit-jupiter-api:${junitVersion}"
	testCompile "org.junit.jupiter:junit-jupiter-engine:${junitVersion}"
	testCompile "org.junit.jupiter:junit-jupiter-params:${junitVersion}"
	testCompile group: 'org.junit.platform', name: 'junit-platform-launcher', version: '1.2.0'
}

configurations {
    all*.exclude group: 'javassist', module: 'javassist'
}

log4j2.yaml:

Configuration:
  status: WARN
  appenders:    
    NoSql:
      name: databaseAppender
      MongoDb3:
        databaseName: tracker
        collectionName: appLog
        server: ds261755.mlab.com
        port: 61755
        username: admin
        password: xxxx
        
  Loggers:
    logger:
      -
        name: com.memorynotfound
        level: info
      -
        name: com.mchange.v2.c3p0
        level: warn
    Root:
      level: info
      AppenderRef:
        ref: databaseAppender

mensagem de erro:

2018-08-14 10:29:26,690 main ERROR Unable to locate plugin type for MongoDb3
2018-08-14 10:29:26,703 main ERROR Unable to locate plugin for MongoDb3
2018-08-14 10:29:26,753 main ERROR Could not create plugin of type class org.apache.logging.log4j.core.appender.nosql.NoSqlAppender for element NoSql: java.lang.NullPointerException java.lang.NullPointerException
	at org.apache.logging.log4j.core.config.plugins.visitors.PluginElementVisitor.findNamedNode(PluginElementVisitor.java:103)
	at org.apache.logging.log4j.core.config.plugins.visitors.PluginElementVisitor.visit(PluginElementVisitor.java:87)
	at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.injectFields(PluginBuilder.java:181)
	at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.build(PluginBuilder.java:122)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.createPluginObject(AbstractConfiguration.java:959)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:899)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:891)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.doConfigure(AbstractConfiguration.java:514)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.initialize(AbstractConfiguration.java:238)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.start(AbstractConfiguration.java:250)
	at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:547)
	at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:619)
	at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:636)
	at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:231)
	at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:153)
	at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:45)
	at org.apache.logging.log4j.LogManager.getContext(LogManager.java:194)
	at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:581)
	at br.com.serversocket.main.Main.<clinit>(Main.java:15)

2018-08-14 10:29:26,764 main ERROR Unable to invoke factory method in class org.apache.logging.log4j.core.appender.nosql.NoSqlAppender for element NoSql: java.lang.IllegalStateException: No factory method found for class org.apache.logging.log4j.core.appender.nosql.NoSqlAppender java.lang.IllegalStateException: No factory method found for class org.apache.logging.log4j.core.appender.nosql.NoSqlAppender
	at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.findFactoryMethod(PluginBuilder.java:235)
	at org.apache.logging.log4j.core.config.plugins.util.PluginBuilder.build(PluginBuilder.java:135)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.createPluginObject(AbstractConfiguration.java:959)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:899)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.createConfiguration(AbstractConfiguration.java:891)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.doConfigure(AbstractConfiguration.java:514)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.initialize(AbstractConfiguration.java:238)
	at org.apache.logging.log4j.core.config.AbstractConfiguration.start(AbstractConfiguration.java:250)
	at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:547)
	at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:619)
	at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:636)
	at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:231)
	at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:153)
	at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:45)
	at org.apache.logging.log4j.LogManager.getContext(LogManager.java:194)
	at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:581)
	at br.com.serversocket.main.Main.<clinit>(Main.java:15)

2018-08-14 10:29:26,773 main ERROR Null object returned for NoSql in appenders.
2018-08-14 10:29:26,813 main ERROR Unable to locate appender "databaseAppender" for logger config "root"

investiguei melhor dentro do jar do log4j-core-2.11.1 e achei o ponto onde o problema está acontecendo:

protected void preConfigure(final Node node) {
    try {
        for (final Node child : node.getChildren()) {
            if (child.getType() == null) { // o problema acontece aqui
                LOGGER.error("Unable to locate plugin type for " + child.getName());
                continue;
            }
            final Class<?> clazz = child.getType().getPluginClass();
            if (clazz.isAnnotationPresent(Scheduled.class)) {
                configurationScheduler.incrementScheduledItems();
            }
            preConfigure(child);
        }
    } catch (final Exception ex) {
        LOGGER.error("Error capturing node data for node " + node.getName(), ex);
    }
}

pelo que entendi no eclipse ele consegue identificar o tipo do node e inferir o tipo do jar do log4j-mongodb3-2.11.1 mas no jar em produção ele não consegue achar a classe do tipo do nó e acontece o problema, verifiquei o jar gerado pelo eclipse e a classe que precisa ser inferida está contida no jar sem nenhum problema.

Descobri o problema, fiz um projeto de testes, sem usar o gradle, e gerei o jar, descobri que preciso copiar as dependências para meu runnable jar e não extrair as dependências dentro dele, alguém sabe como posso configurar o gradle para copiar invés de extrair as dependências ?

Depois de quebrar muito a cabeça achei a solução para incluir os jars sem extrair dentro do runnable jar:

build.gradle (antes)

jar {
    //dependsOn 'test'
    archiveName = "ServerSocket.jar"
    from {
	configurations.runtime.collect {
		    it.isDirectory() ? it : zipTree(it)
	    }

        configurations.compile.collect {
            it.isDirectory() ? it : zipTree(it)
        }
    }

    manifest {
        attributes 'Main-Class': 'br.com.serversocket.main.Main'
    }

    exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA'
}

build.gradle (depois)

jar {
    //dependsOn 'test'
    archiveName = "ServerSocket.jar"
    from {
	configurations.runtime.collect {
		    it.isDirectory() ? it : zipTree(it)
	    }

        configurations.compile.collect {
            it
        }
    }

    manifest {
        attributes 'Main-Class': 'br.com.serversocket.main.Main'
    }

    exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA'
}

só que agora estou recebendo uma exceção de classe não encontrada no projeto:

Exception in thread “main” java.lang.NoClassDefFoundError: org/apache/logging/log4j/LogManager
at br.com.serversocket.main.Main.(Main.java:15)
Caused by: java.lang.ClassNotFoundException: org.apache.logging.log4j.LogManager
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
… 1 more

Pesquisei um pouco e falam que precisa incluir as dependencias do log4j, porém no meu build.gradle já tem todos os jars necessários e dentro da ide o projeto roda sem problemas.

consegui resolver meu problema, tive que usar 2 plugins do gradle para conseguir gerar meu jar:

shadow:
http://imperceptiblethoughts.com/shadow/#shadowing_gradle_plugins

e um plugin adicional para corrigir um bug do shadow em projetos que usam o log4j:

segue meu build.gradle:

buildscript {
    repositories {
        jcenter()
    }
    dependencies {
        classpath 'com.github.jengelman.gradle.plugins:shadow:2.0.4'
        classpath 'de.sebastianboegl.gradle.plugins:shadow-log4j-transformer:2.2.0'
    }
}

apply plugin: 'java'
apply plugin: 'application'
apply plugin: 'eclipse'
apply plugin: 'com.github.johnrengelman.shadow'
archivesBaseName = 'ServerSocket'
version = '3.2.1'

mainClassName = 'br.com.serversocket.main.Main'

compileTestJava {
 	sourceCompatibility = 1.8
	targetCompatibility = 1.8
}

compileJava {
	sourceCompatibility = 1.7
	targetCompatibility = 1.7
}

shadowJar {
    //dependsOn 'test'
    transform(de.sebastianboegl.gradle.plugins.shadow.transformers.Log4j2PluginsFileTransformer)
    archiveName = "ServerSocket.jar"
    
    manifest {
        attributes 'Main-Class': 'br.com.serversocket.main.Main'
    }

    exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA'
}

jar {
    //dependsOn 'test'
    archiveName = "ServerSocket.jar"
	from {
		configurations.runtime.collect {
			it.isDirectory() ? it : zipTree(it)
		}

        configurations.compile.collect {
            it.isDirectory() ? it : zipTree(it)
        }
    }

    manifest {
        attributes 'Main-Class': 'br.com.serversocket.main.Main'
    }

    exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA'
}

test{
	useJUnitPlatform()
	dependsOn 'cleanTest'

    testLogging {
        events "passed", "skipped", "failed"
    }
    afterTest { desc, result -> 
        logger.quiet "Executing test ${desc.name} [${desc.className}] with result: ${result.resultType}"
    }
    testLogging {
        exceptionFormat = 'full'
    }	
}

eclipse.classpath.file.whenMerged {
  entries.each { println it.path }
}
configurations { 
	providedCompile 
}

repositories {
    mavenCentral()
    mavenLocal()
}

ext {
	jacksonVersion = '2.9.1'
	hibernateVerison = '5.1.0.Final'
	slf4jVerison = '1.7.25'
	log4jVerison = '2.11.1'
	junitVersion = '5.2.0'
	emailVersion = '1.6.1'
	mongoDBVersion = '3.8.0'
}

dependencies {
	
	//compile files(fileTree(dir: 'lib', includes: ['*.jar']))	
	compile "org.hibernate:hibernate-jpamodelgen:${hibernateVerison}"
	compile "org.hibernate:hibernate-c3p0:${hibernateVerison}"
	compile "org.hibernate:hibernate-core:${hibernateVerison}"
	compile "org.hibernate:hibernate-entitymanager:${hibernateVerison}"
	
	compile "org.slf4j:slf4j-simple:${slf4jVerison}"
	compile "org.slf4j:slf4j-api:${slf4jVerison}"
	
	compile "org.apache.logging.log4j:log4j-api:${log4jVerison}"
	compile "org.apache.logging.log4j:log4j-core:${log4jVerison}"
	compile "org.apache.logging.log4j:log4j-mongodb3:${log4jVerison}"
	
	
	compile "com.fasterxml.jackson.core:jackson-core:${jacksonVersion}"
	compile "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}"
	compile "com.fasterxml.jackson.core:jackson-annotations:${jacksonVersion}"
	compile "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:${jacksonVersion}"
	
	compile "javax.mail:javax.mail-api:${emailVersion}"
	compile "com.sun.mail:javax.mail:${emailVersion}"
	
	compile "org.mongodb:mongodb-driver:${mongoDBVersion}"
	compile "org.mongodb:mongodb-driver-core:${mongoDBVersion}"
	compile "org.mongodb:bson:${mongoDBVersion}"
	
	
	compile group: 'org.projectlombok', name: 'lombok', version: '1.18.2'
	compile group: 'org.yaml', name: 'snakeyaml', version: '1.21'

	compile group: 'mysql', name: 'mysql-connector-java', version: '5.1.44'
	compile group: 'org.hibernate.common', name: 'hibernate-commons-annotations', version: '5.0.1.Final'
	compile group: 'org.hibernate.javax.persistence', name: 'hibernate-jpa-2.1-api', version: '1.0.2.Final'
	compile group: 'com.mchange', name: 'c3p0', version: '0.9.2.1'
	compile group: 'org.eclipse.persistence', name: 'javax.persistence', version: '2.1.0'
	compile group: 'org.jboss.logging', name: 'jboss-logging', version: '3.3.1.Final'
	compile group: 'commons-logging', name: 'commons-logging', version: '1.0.3'
	compile group: 'org.apache.mina', name: 'mina-core', version: '2.0.19'
	compile group: 'antlr', name: 'antlr', version: '2.7.7'
	compile group: 'com.fasterxml', name: 'classmate', version: '1.3.0'
	compile group: 'commons-codec', name: 'commons-codec', version: '1.11'
	compile group: 'commons-beanutils', name: 'commons-beanutils', version: '1.6'
	compile group: 'commons-collections', name: 'commons-collections', version: '3.2.1'
	compile group: 'org.apache.commons', name: 'commons-email', version: '1.5'
	compile group: 'commons-httpclient', name: 'commons-httpclient', version: '3.1'
	compile group: 'commons-lang', name: 'commons-lang', version: '2.3'
	compile group: 'commons-discovery', name: 'commons-discovery', version: '0.2'
	compile group: 'dom4j', name: 'dom4j', version: '1.6.1'
	compile group: 'net.sf.ehcache', name: 'ehcache', version: '1.5.0'
	compile group: 'org.apache.geronimo.specs', name: 'geronimo-jta_1.1_spec', version: '1.1.1'
	compile group: 'org.jboss', name: 'jandex', version: '2.0.3.Final'
	compile group: 'org.javassist', name: 'javassist', version: '3.22.0-GA'
	compile group: 'jdom', name: 'jdom', version: '1.1'
	compile group: 'javax.transaction', name: 'jta', version: '1.1'
	compile group: 'com.vividsolutions', name: 'jts', version: '1.13'
	compile group: 'org.apache.axis', name: 'axis', version: '1.4'
	compile group: 'axis', name: 'axis-jaxrpc', version: '1.4'
	compile group: 'javax.xml.soap', name: 'saaj-api', version: '1.3'
	compile group: 'wsdl4j', name: 'wsdl4j', version: '1.6.2'
	compile group: 'com.mchange', name: 'mchange-commons-java', version: '0.2.3.4'


	testCompile group: 'com.h2database', name: 'h2', version: '1.4.197'
	testCompile "org.junit.jupiter:junit-jupiter-api:${junitVersion}"
	testCompile "org.junit.jupiter:junit-jupiter-engine:${junitVersion}"
	testCompile "org.junit.jupiter:junit-jupiter-params:${junitVersion}"
	testCompile group: 'org.junit.platform', name: 'junit-platform-launcher', version: '1.2.0'
}

configurations {
    all*.exclude group: 'javassist', module: 'javassist'
}