Error during tomcat startup for log4j2.16 upgrade to an existing spring mvc application

Question

I'm trying to upgrade log4j from 1.2.17 to log4j2.16. We use spring mvc 4.2.1.RELEASE. Here is my pom.xml

    <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
  <modelVersion>4.0.0</modelVersion>
  <groupId>com.springapp</groupId>
  <artifactId>app</artifactId>
  <packaging>war</packaging>
  <version>1.0-SNAPSHOT</version>
  <name>App</name>
  <repositories>
    <repository>
      <id>atlassian-repo</id>
      <url>https://maven.atlassian.com/repository/public</url>
    </repository>
    <repository>
      <id>sshtools</id>
      <name>sshtools-releases</name>
      <url>http://artifactory.javassh.com/public-releases</url>
    </repository>
  </repositories>
  <properties>
    <spring.version>4.2.1.RELEASE</spring.version>
    <spring.jpa.version>1.5.3.RELEASE</spring.jpa.version>
    <tiles.version>3.0.1</tiles.version>
    <jackson.version>1.9.10</jackson.version>
    <prometheus.version>0.6.0</prometheus.version>
  </properties>

  <dependencies>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-compress</artifactId>
      <version>1.19</version>
    </dependency>
    <dependency>
      <groupId>ch.ethz.ganymed</groupId>
      <artifactId>ganymed-ssh2</artifactId>
      <version>262</version>
    </dependency>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-lang3</artifactId>
      <version>3.4</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-core</artifactId>
      <version>${spring.version}</version>
    </dependency>

    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-jms</artifactId>
      <version>${spring.version}</version>
    </dependency>


    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-web</artifactId>
      <version>${spring.version}</version>
      <exclusions>
        <exclusion>
          <artifactId>commons-logging</artifactId>
          <groupId>commons-logging</groupId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-orm</artifactId>
      <version>${spring.version}</version>
    </dependency>

    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-websocket</artifactId>
      <version>${spring.version}</version>
    </dependency>

    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-messaging</artifactId>
      <version>${spring.version}</version>
    </dependency>

    <dependency>
      <groupId>javax.servlet</groupId>
      <artifactId>servlet-api</artifactId>
      <version>2.5</version>
    </dependency>

    <dependency>
      <groupId>javax.servlet.jsp</groupId>
      <artifactId>jsp-api</artifactId>
      <version>2.1</version>
      <scope>provided</scope>
    </dependency>

    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-webmvc</artifactId>
      <version>${spring.version}</version>
    </dependency>

    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-test</artifactId>
      <version>${spring.version}</version>
      <scope>test</scope>
    </dependency>

    <dependency>
      <groupId>org.apache.logging.log4j</groupId>
      <artifactId>log4j-api</artifactId>
      <version>2.16.0</version>
    </dependency>
    <dependency>
      <groupId>org.apache.logging.log4j</groupId>
      <artifactId>log4j-core</artifactId>
      <version>2.16.0</version>
    </dependency>
    <dependency>
      <groupId>org.apache.logging.log4j</groupId>
      <artifactId>log4j-slf4j-impl</artifactId>
      <version>2.16.0</version>
      <!--<exclusions>
        <exclusion>
          <artifactId>slf4j-api</artifactId>
          <groupId>org.slf4j</groupId>
        </exclusion>
      </exclusions>-->
    </dependency>
    <dependency>
      <groupId>org.apache.logging.log4j</groupId>
      <artifactId>log4j-web</artifactId>
      <version>2.16.0</version>
    </dependency>


    <dependency>
      <groupId>org.hibernate</groupId>
      <artifactId>hibernate-core</artifactId>
      <version>4.3.6.Final</version>
    </dependency>

    <dependency>
      <groupId>org.hibernate</groupId>
      <artifactId>hibernate-entitymanager</artifactId>
      <version>4.3.6.Final</version>
    </dependency>

    <dependency>
      <groupId>mysql</groupId>
      <artifactId>mysql-connector-java</artifactId>
      <version>5.1.30</version>
    </dependency>

    <dependency>
      <groupId>javax.inject</groupId>
      <artifactId>javax.inject</artifactId>
      <version>1</version>
    </dependency>

    <dependency>
      <groupId>javax.enterprise</groupId>
      <artifactId>cdi-api</artifactId>
      <version>1.1</version>
    </dependency>


    <dependency>
      <groupId>org.apache.geronimo.specs</groupId>
      <artifactId>geronimo-servlet_3.0_spec</artifactId>
      <version>1.0</version>
      <scope>test</scope>
    </dependency>

    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.8.2</version>
      <scope>test</scope>
    </dependency>

    <dependency>
      <groupId>org.apache.tiles</groupId>
      <artifactId>tiles-template</artifactId>
      <version>${tiles.version}</version>
    </dependency>

    <dependency>
      <groupId>org.apache.tiles</groupId>
      <artifactId>tiles-el</artifactId>
      <version>${tiles.version}</version>
    </dependency>

    <dependency>
      <groupId>org.apache.tiles</groupId>
      <artifactId>tiles-jsp</artifactId>
      <version>${tiles.version}</version>
    </dependency>

    <dependency>
      <groupId>org.apache.tiles</groupId>
      <artifactId>tiles-servlet</artifactId>
      <version>${tiles.version}</version>
    </dependency>

    <dependency>
      <groupId>org.apache.tiles</groupId>
      <artifactId>tiles-el</artifactId>
      <version>${tiles.version}</version>
    </dependency>

    <dependency>
      <groupId>org.apache.tiles</groupId>
      <artifactId>tiles-core</artifactId>
      <version>${tiles.version}</version>
      <exclusions>
        <exclusion>
          <artifactId>jcl-over-slf4j</artifactId>
          <groupId>org.slf4j</groupId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>org.apache.tiles</groupId>
      <artifactId>tiles-api</artifactId>
      <version>${tiles.version}</version>
    </dependency>

    <dependency>
      <groupId>jstl</groupId>
      <artifactId>jstl</artifactId>
      <version>1.2</version>
    </dependency>
    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-jdbc</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>org.postgresql</groupId>
      <artifactId>postgresql</artifactId>
      <version>42.2.22</version>
      <exclusions>
        <exclusion>
          <groupId>org.slf4j</groupId>
          <artifactId>slf4j-simple</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <!-- Jackson -->
    <dependency>
      <groupId>org.codehaus.jackson</groupId>
      <artifactId>jackson-mapper-asl</artifactId>
      <version>${jackson.version}</version>
    </dependency>

    <dependency>
      <groupId>org.modelmapper</groupId>
      <artifactId>modelmapper</artifactId>
      <version>0.7.2</version>
    </dependency>

    <dependency>
      <groupId>org.hibernate</groupId>
      <artifactId>hibernate-validator</artifactId>
      <version>5.1.2.Final</version>
    </dependency>

    <dependency>
      <groupId>javax.validation</groupId>
      <artifactId>validation-api</artifactId>
      <version>1.1.0.Final</version>
    </dependency>

    <dependency>
      <groupId>com.jcraft</groupId>
      <artifactId>jsch</artifactId>
      <version>0.1.51</version>
    </dependency>

    <dependency>
      <groupId>org.codehaus.jettison</groupId>
      <artifactId>jettison</artifactId>
      <version>1.3.4</version>
    </dependency>

    <dependency>
      <groupId>com.sun.xml.bind</groupId>
      <artifactId>jaxb-impl</artifactId>
      <version>2.1.12</version>
    </dependency>
    <dependency>
      <groupId>javax.activation</groupId>
      <artifactId>activation</artifactId>
      <version>1.1</version>
    </dependency>
    <dependency>
      <groupId>javax.ws.rs</groupId>
      <artifactId>jsr311-api</artifactId>
      <version>1.1.1</version>
    </dependency>
    <dependency>
      <groupId>javax.xml</groupId>
      <artifactId>jaxb-api</artifactId>
      <version>2.1</version>
    </dependency>
    <dependency>
      <groupId>javax.xml.stream</groupId>
      <artifactId>stax-api</artifactId>
      <version>1.0-2</version>
    </dependency>
    <dependency>
      <groupId>stax</groupId>
      <artifactId>stax-api</artifactId>
      <version>1.0.1</version>
    </dependency>
    <dependency>
      <groupId>com.google.guava</groupId>
      <artifactId>guava</artifactId>
      <version>18.0</version>
    </dependency>
    <dependency>
      <groupId>joda-time</groupId>
      <artifactId>joda-time</artifactId>
      <version>1.6.2</version>
    </dependency>
    <dependency>
      <groupId>com.google.code.findbugs</groupId>
      <artifactId>jsr305</artifactId>
      <version>3.0.0</version>
    </dependency>
    <dependency>
      <groupId>com.jcraft</groupId>
      <artifactId>jsch</artifactId>
      <version>0.1.51</version>
    </dependency>
    <dependency>
      <groupId>com.sun.jersey</groupId>
      <artifactId>jersey-client</artifactId>
      <version>1.5</version>
    </dependency>
    <dependency>
      <groupId>com.sun.jersey</groupId>
      <artifactId>jersey-core</artifactId>
      <version>1.18.1</version>
    </dependency>
    <dependency>
      <groupId>com.sun.jersey</groupId>
      <artifactId>jersey-json</artifactId>
      <version>1.18.1</version>
    </dependency>
    <dependency>
      <groupId>com.sun.jersey.contribs</groupId>
      <artifactId>jersey-multipart</artifactId>
      <version>1.18</version>
    </dependency>
    <dependency>
      <groupId>com.sun.jersey.contribs.jersey-oauth</groupId>
      <artifactId>oauth-client</artifactId>
      <version>1.18.1</version>
    </dependency>
    <dependency>
      <groupId>com.sun.jersey.contribs.jersey-oauth</groupId>
      <artifactId>oauth-signature</artifactId>
      <version>1.18.1</version>
    </dependency>

    <dependency>
      <groupId>com.atlassian.jira</groupId>
      <artifactId>jira-rest-java-client</artifactId>
      <version>1.1-m02</version>
    </dependency>

    <dependency>
      <groupId>com.fasterxml.jackson.core</groupId>
      <artifactId>jackson-databind</artifactId>
      <version>2.9.8</version>
    </dependency>

    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-messaging</artifactId>
      <version>${spring.version}</version>
    </dependency>

    <dependency>
      <groupId>org.springframework</groupId>
      <artifactId>spring-websocket</artifactId>
      <version>${spring.version}</version>
    </dependency>
    <dependency>
      <groupId>javax.servlet</groupId>
      <artifactId>javax.servlet-api</artifactId>
      <version>3.0.1</version>
    </dependency>

    <dependency>
      <groupId>net.sf.jsqlparser</groupId>
      <artifactId>jsqlparser</artifactId>
      <version>0.8.0</version>
    </dependency>
    

    <dependency>
      <groupId>com.itextpdf</groupId>
      <artifactId>itextpdf</artifactId>
      <version>5.0.6</version>
    </dependency>

    <dependency>
      <groupId>org.apache.pdfbox</groupId>
      <artifactId>pdfbox</artifactId>
      <version>2.0.4</version>
    </dependency>

    <dependency>
      <groupId>com.github.dhorions</groupId>
      <artifactId>boxable</artifactId>
      <version>1.6</version>
      <exclusions>
        <exclusion>
          <artifactId>slf4j-api</artifactId>
          <groupId>org.slf4j</groupId>
        </exclusion>
      </exclusions>
    </dependency>


    <!-- Apache Commons Upload -->
    <dependency>
      <groupId>commons-fileupload</groupId>
      <artifactId>commons-fileupload</artifactId>
      <version>1.3.1</version>
    </dependency>

    <!-- Apache Commons Upload -->
    <dependency>
      <groupId>commons-io</groupId>
      <artifactId>commons-io</artifactId>
      <version>2.4</version>
    </dependency>

    <dependency>
      <groupId>com.codesnippets4all</groupId>
      <artifactId>quick-json</artifactId>
      <version>1.0.4</version>
    </dependency>

    <dependency>
      <groupId>org.jasypt</groupId>
      <artifactId>jasypt</artifactId>
      <version>1.9.2</version>
    </dependency>

    <dependency>
      <groupId>net.sf.opencsv</groupId>
      <artifactId>opencsv</artifactId>
      <version>2.3</version>
    </dependency>

    <dependency>
      <groupId>org.powermock</groupId>
      <artifactId>powermock-module-junit4</artifactId>
      <version>1.6.2</version>
    </dependency>

    <dependency>
      <groupId>org.powermock</groupId>
      <artifactId>powermock-api-mockito</artifactId>
      <version>1.6.2</version>
    </dependency>

    <dependency>
      <groupId>org.aspectj</groupId>
      <artifactId>aspectjrt</artifactId>
      <version>1.8.1</version>
    </dependency>

    <dependency>
      <groupId>org.aspectj</groupId>
      <artifactId>aspectjweaver</artifactId>
      <version>1.8.1</version>
    </dependency>

    <dependency>
      <groupId>org.apache.activemq</groupId>
      <artifactId>activemq-core</artifactId>
      <version>5.7.0</version>
      <exclusions>
        <exclusion>
          <artifactId>slf4j-api</artifactId>
          <groupId>org.slf4j</groupId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>com.google.code.gson</groupId>
      <artifactId>gson</artifactId>
      <version>2.7</version>
    </dependency>

    <!-- ecache dependencies -->
    <!-- EHCache Core APIs -->
    <dependency>
      <groupId>net.sf.ehcache</groupId>
      <artifactId>ehcache</artifactId>
      <version>2.9.0</version>
      <exclusions>
        <exclusion>
          <artifactId>slf4j-api</artifactId>
          <groupId>org.slf4j</groupId>
        </exclusion>
      </exclusions>
    </dependency>


    <dependency>
      <groupId>io.fabric8</groupId>
      <artifactId>kubernetes-client</artifactId>
      <version>4.3.0</version>
      <exclusions>
        <exclusion>
          <artifactId>slf4j-api</artifactId>
          <groupId>org.slf4j</groupId>
        </exclusion>
      </exclusions>
    </dependency>

    <!-- https://mvnrepository.com/artifact/javax.mail/mail -->
    <dependency>
      <groupId>javax.mail</groupId>
      <artifactId>mail</artifactId>
      <version>1.4</version>
    </dependency>

    <!-- https://mvnrepository.com/artifact/org.flywaydb/flyway-core -->
    <dependency>
      <groupId>org.flywaydb</groupId>
      <artifactId>flyway-core</artifactId>
      <version>6.3.1</version>
    </dependency>


    <!-- https://mvnrepository.com/artifact/org.rauschig/jarchivelib -->
    <dependency>
      <groupId>org.rauschig</groupId>
      <artifactId>jarchivelib</artifactId>
      <version>0.7.0</version>
    </dependency>

    <dependency>
      <groupId>org.jsoup</groupId>
      <artifactId>jsoup</artifactId>
      <version>1.8.3</version>
    </dependency>

    <dependency>
      <groupId>org.apache.httpcomponents</groupId>
      <artifactId>httpclient</artifactId>
      <version>4.5</version>
    </dependency>
    <dependency>
      <groupId>org.apache.httpcomponents</groupId>
      <artifactId>httpmime</artifactId>
      <version>4.5</version>
    </dependency>
    <!-- https://mvnrepository.com/artifact/redis.clients/jedis -->
    <dependency>
      <groupId>redis.clients</groupId>
      <artifactId>jedis</artifactId>
      <version>2.9.0</version>
    </dependency>

    <dependency>
      <groupId>com.gsql</groupId>
      <artifactId>gsql</artifactId>
      <version>1.0</version>
    </dependency>

    <!-- https://mvnrepository.com/artifact/com.microsoft.sqlserver/sqljdbc4 -->
    <dependency>
      <groupId>com.microsoft.sqlserver</groupId>
      <artifactId>sqljdbc4</artifactId>
      <version>4.0</version>
    </dependency>

    <dependency>
      <groupId>org.projectlombok</groupId>
      <artifactId>lombok</artifactId>
      <version>1.16.20</version>
    </dependency>

    <dependency>
      <groupId>org.springframework.data</groupId>
      <artifactId>spring-data-jpa</artifactId>
      <version>${spring.jpa.version}</version>
      <exclusions>
        <exclusion>
          <artifactId>slf4j-api</artifactId>
          <groupId>org.slf4j</groupId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>jcifs</groupId>
      <artifactId>jcifs</artifactId>
      <version>1.3.17</version>
    </dependency>

    <dependency>
      <groupId>io.jsonwebtoken</groupId>
      <artifactId>jjwt</artifactId>
      <version>0.6.0</version>
    </dependency>

    <dependency>
      <groupId>org.javers</groupId>
      <artifactId>javers-core</artifactId>
      <version>5.0.1</version>
      <exclusions>
        <exclusion>
          <artifactId>slf4j-api</artifactId>
          <groupId>org.slf4j</groupId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>org.eclipse.jgit</groupId>
      <artifactId>org.eclipse.jgit</artifactId>
      <version>5.2.0.201812061821-r</version>
      <exclusions>
        <exclusion>
          <artifactId>slf4j-api</artifactId>
          <groupId>org.slf4j</groupId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>org.apache.poi</groupId>
      <artifactId>poi</artifactId>
      <version>4.1.0</version>
    </dependency>
    <dependency>
      <groupId>org.apache.poi</groupId>
      <artifactId>poi-ooxml</artifactId>
      <version>4.1.0</version>
    </dependency>
    <dependency>
      <groupId>net.sf.supercsv</groupId>
      <artifactId>super-csv</artifactId>
      <version>2.1.0</version>
    </dependency>
    

    <dependency>
      <groupId>org.apache.httpcomponents</groupId>
      <artifactId>httpclient</artifactId>
      <version>4.5.6</version>
    </dependency>
    <dependency>
      <groupId>org.apache.httpcomponents</groupId>
      <artifactId>fluent-hc</artifactId>
      <version>4.5.9</version>
    </dependency>

    <dependency>
      <groupId>org.json</groupId>
      <artifactId>json</artifactId>
      <version>20180813</version>
    </dependency>

  </dependencies>


  
  </build>
</project>

I'm getting the following error:

    WEB-INF/lib/log4j-core-2.16.0.jar!/] for annotations
 java.io.EOFException
    at java.io.DataInputStream.readUnsignedShort(DataInputStream.java:340)
    at org.apache.tomcat.util.bcel.classfile.Utility.swallowMethodParameters(Utility.java:188)
    at org.apache.tomcat.util.bcel.classfile.Attribute.readAttribute(Attribute.java:159)
    at org.apache.tomcat.util.bcel.classfile.FieldOrMethod.<init>(FieldOrMethod.java:76)
    at org.apache.tomcat.util.bcel.classfile.ClassParser.readMethods(ClassParser.java:226)
    at org.apache.tomcat.util.bcel.classfile.ClassParser.parse(ClassParser.java:101)
    at org.apache.catalina.startup.ContextConfig.processAnnotationsStream(ContextConfig.java:1987)
    at org.apache.catalina.startup.ContextConfig.processAnnotationsJar(ContextConfig.java:1940)
    at org.apache.catalina.startup.ContextConfig.processAnnotationsUrl(ContextConfig.java:1915)
    at org.apache.catalina.startup.ContextConfig.processAnnotations(ContextConfig.java:1876)
    at org.apache.catalina.startup.ContextConfig.webConfig(ContextConfig.java:1145)
    at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:767)
    at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:302)
    at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)
    at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5083)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:724)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:700)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:714)
    at org.apache.catalina.startup.HostConfig.manageApp(HostConfig.java:1588)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:300)
    at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)