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com.typesafe.config.ConfigException$Missing: reference.conf: No configuration setting found for key 'default'

I created a jar file of my Akka application. When I run the jar file by the command
java -jar file.jar
then I see this error. What could be possibly wrong and how can I fix this?
[ERROR] [04/28/2022 14:11:03.296] [main] [KnowledgePortalRest(akka://knowledge-portal-actor-system)] Error starting application:
com.typesafe.config.ConfigException$Missing: reference.conf # jar:file:/home/knoldus/knolx-service/target/scala-2.12/sbt-1.0/knowledge-portal-rest-assembly-2.2.1.jar!/reference.conf: 13-1466: No configuration setting found for key 'default'
at com.typesafe.config.impl.SimpleConfig.findKeyOrNull(SimpleConfig.java:156)
at com.typesafe.config.impl.SimpleConfig.findOrNull(SimpleConfig.java:174)
at com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:188)
at com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:193)
at com.typesafe.config.impl.SimpleConfig.getBoolean(SimpleConfig.java:218)
at com.typesafe.sslconfig.util.ConfigLoader$.$anonfun$booleanLoader$2(Configuration.scala:186)
at com.typesafe.sslconfig.util.ConfigLoader$.$anonfun$booleanLoader$2$adapted(Configuration.scala:186)
at com.typesafe.sslconfig.util.ConfigLoader$$anon$2.load(Configuration.scala:173)
at com.typesafe.sslconfig.util.EnrichedConfig.get(Configuration.scala:22)
at com.typesafe.sslconfig.ssl.SSLConfigParser.parse(Config.scala:498)
at com.typesafe.sslconfig.ssl.SSLConfigFactory$.parse(Config.scala:486)
at com.typesafe.sslconfig.akka.AkkaSSLConfig$.defaultSSLConfigSettings(AkkaSSLConfig.scala:34)
at com.typesafe.sslconfig.akka.AkkaSSLConfig$.createExtension(AkkaSSLConfig.scala:29)
at com.typesafe.sslconfig.akka.AkkaSSLConfig$.createExtension(AkkaSSLConfig.scala:19)
at akka.actor.ActorSystemImpl.registerExtension(ActorSystem.scala:1006)
at akka.actor.ExtensionId.apply(Extension.scala:79)
at akka.actor.ExtensionId.apply$(Extension.scala:78)
at com.typesafe.sslconfig.akka.AkkaSSLConfig$.apply(AkkaSSLConfig.scala:24)
at com.typesafe.sslconfig.akka.AkkaSSLConfig$.apply(AkkaSSLConfig.scala:19)
at akka.http.scaladsl.HttpExt.<init>(Http.scala:82)
at akka.http.scaladsl.Http$.createExtension(Http.scala:1132)
at akka.http.scaladsl.Http$.createExtension(Http.scala:901)
at akka.actor.ActorSystemImpl.registerExtension(ActorSystem.scala:1006)
at akka.actor.ExtensionId.apply(Extension.scala:79)
at akka.actor.ExtensionId.apply$(Extension.scala:78)
at akka.http.scaladsl.Http$.apply(Http.scala:1127)
at com.knoldus.HttpServer.start(HttpServer.scala:28)
at com.knoldus.HttpServerApp$.delayedEndpoint$com$knoldus$HttpServerApp$1(HttpServerApp.scala:70)
at com.knoldus.HttpServerApp$delayedInit$body.apply(HttpServerApp.scala:24)
at scala.Function0.apply$mcV$sp(Function0.scala:39)
at scala.Function0.apply$mcV$sp$(Function0.scala:39)
at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:17)
at scala.App.$anonfun$main$1$adapted(App.scala:80)
at scala.collection.immutable.List.foreach(List.scala:392)
at scala.App.main(App.scala:80)
at scala.App.main$(App.scala:78)
at com.knoldus.HttpServerApp$.main(HttpServerApp.scala:24)
at com.knoldus.HttpServerApp.main(HttpServerApp.scala)

This kind of error happens when the application is unable to found the reference.conf configuration file in the classpath.
Make sure such file is present in the jar you've built.

glassfish 4.1 class org.springframework.beans.factory.BeanCreationException

please help, this is very confusing, I can't deploy my war file in glassfish (where previously it could) with an error message like this
"https://localhost:4848/management/domain/applications/application/myApp"
created successfully. Warning: Command _deploy did not complete
successfully on server instance instance1: remote failure: Failed to
load the application on instance instance1. The application will not
run properly. Please fix your application and redeploy. Exception
while loading the app : java.lang.IllegalStateException:
ContainerBase.addChild: start: org.apache.catalina.LifecycleException:
java.lang.NoClassDefFoundError: Could not initialize class
org.springframework.beans.factory.BeanCreationException. Please see
server.log for more details. Warning: Command _deploy did not complete
successfully on server instance instance1: remote failure: Failed to
load the application on instance instance1. The application will not
run properly. Please fix your application and redeploy. Exception
while loading the app : java.lang.IllegalStateException:
ContainerBase.addChild: start: org.apache.catalina.Lifecycle ....
msg.seeServerLog
glassfish : 4.1
java version : 1.7.0_121
os : ubuntu server 12
I also could not find meaningful information in the server.log
but my war file can work well on my local tomcat
I'm sure there is no duplicates lib, because it was previously running well and indeed there was no change in my lib

Websphere Error SRVE0206E SRVE0187E SRVE0234I SRVE0266E

I'm currently wasting my time trying to figure out why WAS won't load my EAR and why said EAR have problem.
Context:
One of my colleague updated a version of a jar and then my m2e seem to have not picked up and was giving thousand of error (was working fine before)
I tried to check if it was Nexus (work fine). My encrypted password in the setting.xml (work fine).
I decided to try maven from the command line, everything worked fine there to.
When I tried again in RAD (IBM eclipse) everything was now ok, no more error.
I then proceeded to put the generated EAR in my websphere server via add and remove project and I get multiple error when I try to start the server with that ear. (see below)
I though that because it was compiled via maven cmd prompt, I might have compiled with the wrong jvm or something so I deleted my maven repo (.m2 in the user) and try to get the jar via m2e in RAD only.
It's worked until I started the server with the new EAR and got the same set of error.
Any idea on what to do to get rid of these error and have a healthy server.
Here some of the error:
[11/10/17 12:08:51:994 EST] 00000075 annotation W
com.ibm.ws.webcontainer.annotation.WASAnnotationHelper collectClasses
SRVE8000W: Skipped class that failed to initialize for annotation
scanning.
java.lang.ClassNotFoundException: org.springframework.web.servlet.tags.form.SelectTag at
java.lang.Class.forNameImpl(Native Method) at
java.lang.Class.forName(Class.java:219) ...
[11/10/17 12:09:00:282 EST] 00000075 wtp W
org.eclipse.jst.j2ee.commonarchivecore.internal.strategy.TempZipFile
clearTempFile Failed to delete temporary file [
C:\IBM\WebSphere\AppServer-x86\profiles\chris_pro\wstemp\appdepl15fa68a2a21\AuthRenfClientWeb-2.0.26.war2406380505527260260.tmp
] [11/10/17 12:09:00:433 EST] 00000075 SinglePathCla E WSVR0120E: An
error occurred processing com.mycom.bla.testalive.TestAliveServlet
java.io.FileNotFoundException:
C:\IBM\WebSphere\AppServer-x86\profiles\chris_pro\wstemp\appdepl15fa68a2a21\Client-1.61.5-SNAPSHOT.jar6655053587500024283.tmp
(The system cannot find the file specified.) ...
SRVE0266E: Error occured while initializing servlets: {0}
javax.servlet.UnavailableException: SRVE0203E: Servlet [SecurityManager]:
com.mycom.bla.pres.request.http.HttpSecurityManagerServlet was found,
but is missing another required class. SRVE0206E: This error typically
implies that the servlet was originally compiled with classes which
cannot be located by the server. SRVE0187E: Check your class path to
ensure that all classes required by the servlet are present.SRVE0210I:
This problem can be debugged by recompiling the servlet using only the
classes in the application's runtime class path SRVE0234I: Application
class

Sonarqube evaluation - Ant Build failing

Updated to reflect Sonar-Runner
We have these projects configured:
We're using this sonar-project.properties file in the root of the folder containing our application source:
sonar.projectKey=Southern
sonar.projectName=Southern
sonar.projectVersion=1.0
sonar.sources=.
We run the sonar-runner command in the same folder in which the above properties file exists. We get the following error:
ERROR: Error during SonarQube Scanner execution
ERROR: Unable to load component class org.sonar.batch.report.ActiveRulesPublishe
r
ERROR: Caused by: Unable to load component interface org.sonar.api.batch.rule.Ac
tiveRules
ERROR: Caused by: Unable to load component class org.sonar.batch.rule.ModuleQPro
files
ERROR: Caused by: Error 500 on http://localhost:9000/api/qualityprofiles/search.
protobuf?projectKey=Southern
ERROR:
The SonarQube application and website are running and available.

Downloaded the sonar-runner.
Updated properties file: sonar-sources=src. Scans ran but hung with an error that the DB was locked.
Rebooted the machine and restarted SonarQube. Problem resolved. All scans run.

Exception while connecting to Neo4j

Error starting org.neo4j.kernel.EmbeddedGraphDatabase, /home/manish/Softwares/neo4j-enterprise-2.1.6/data/graph.db
CausedBy: Component 'org.neo4j.kernel.impl.transaction.XaDataSourceManager#2a792260' was successfully initialized, but failed to start. Please see attached cause exception.
CausedBy: Component 'org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource#23d7c3d2' was successfully initialized, but failed to start. Please see attached cause exception.
CausedBy : No schema index provider org.neo4j.kernel.api.index.SchemaIndexProvider found. Kernel extensions available on classpath: Class path entries: /home/manish/NetBeansProjects/ClassLibOperations/store/ClassLibNeo4jOperations.jar /home/manish/NetBeansProjects/ClassLib2/store/2.jar /home/manish/NetBeansProjects/ClassLibB/store/3.jar /home/manish/NetBeansProjects/ExecuteJarFile/build/classes
I am getting the above exception while executing the line :
database = new GraphDatabaseFactory().newEmbeddedDatabase( DB_PATH );
The scenario is something like this :
I have a class library for operation with neo4j graph db named ClassLibNeo4jOperations. This class library has all the references required for working with neo4j.
Now I am packaging this ClassLibrary as ClassLibNeo4jOperations.jar and adding it as reference in a Console Application ExecuteJarFile.
Now when i am calling a method of this jar file this line
database = new GraphDatabaseFactory().newEmbeddedDatabase( DB_PATH ); is executed which throws the above mentioned exception.
The JAR (ClassLibNeo4jOperations.jar) is a fat jar ,created using the method mentioned at How to build fat jar

Make sure you have neo4j-lucene-index.jar on your classpath.