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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Exomiser Web - Application run fails #400

Closed GreekByte closed 3 years ago

GreekByte commented 3 years ago

Hello,

I am trying to run the Exomiser Web application but get the error "java.lang.IllegalArgumentException: genomeAnalysisServices cannot be empty" during context initialization.

I built the exomiser-web-12.1.0.jar file with mvn install. I placed the application.properties file in the same folder as the exomiser-web-12.1.0.jar file. In application.properties, I define the data directory:

exomiser.data-directory=/data/fast/exomizer/exomiser-cli-12.1.0/data/2102_hg19

I get the same error when I use this path instead: exomiser.data-directory=/data/fast/exomizer/exomiser-cli-12.1.0/data

The exomiser-client, which I downloaded from https://exomiser.monarchinitiative.org/exomiser/download runs smoothly.

Does the error with the web app mean that it cannot locate the hg19 genome database? Any help is greately appreciated.

Thanks, Stathis

Here is the shell output:

(base) papachristos@man2-dev001:~/projects/Exomiser/exomiser-web/target$ java -jar -XX:+UseG1GC -Xms8G -Xmx8G exomiser-web-12.1.0.jar

| | | _ | __| ____ _ ()__ _ | | | ' \ / \ | | \ \/ / | ' ` | / |/ _ \ '| | | | | | | / | | > < () | | | | | | __ \ _/ | || || ||_| |__//__/|| || |||/\|_|

=== Web Server === v12.1.0

2021-06-18 11:24:53.902 INFO 228750 --- [ main] o.m.exomiser.web.ExomiserWebApp : Starting ExomiserWebApp on man2-dev001 with PID 228750 (/home/papachristos/projects/Exomiser/exomiser-web/target/exomiser-web-12.1.0.jar started by papachristos in /home/papachristos/projects/Exomiser/exomiser-web/target) 2021-06-18 11:24:53.905 INFO 228750 --- [ main] o.m.exomiser.web.ExomiserWebApp : No active profile set, falling back to default profiles: default 2021-06-18 11:24:55.176 INFO 228750 --- [ main] trationDelegate$BeanPostProcessorChecker : Bean 'org.springframework.transaction.annotation.ProxyTransactionManagementConfiguration' of type [org.springframework.transaction.annotation.ProxyTransactionManagementConfiguration$$EnhancerBySpringCGLIB$$9622ef3] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying) 2021-06-18 11:24:55.490 INFO 228750 --- [ main] o.s.b.w.embedded.tomcat.TomcatWebServer : Tomcat initialized with port(s): 8090 (http) 2021-06-18 11:24:55.514 INFO 228750 --- [ main] o.apache.catalina.core.StandardService : Starting service [Tomcat] 2021-06-18 11:24:55.514 INFO 228750 --- [ main] org.apache.catalina.core.StandardEngine : Starting Servlet engine: [Apache Tomcat/9.0.16] 2021-06-18 11:24:55.523 INFO 228750 --- [ main] o.a.catalina.core.AprLifecycleListener : The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/usr/java/packages/lib:/usr/lib64:/lib64:/lib:/usr/lib] 2021-06-18 11:24:55.580 INFO 228750 --- [ main] o.a.c.c.C.[.[localhost].[/exomiser] : Initializing Spring embedded WebApplicationContext 2021-06-18 11:24:55.580 INFO 228750 --- [ main] o.s.web.context.ContextLoader : Root WebApplicationContext: initialization completed in 1638 ms 2021-06-18 11:24:55.992 INFO 228750 --- [ main] o.m.e.web.config.ControllerConfig : Set max variants to 100000 2021-06-18 11:24:55.994 INFO 228750 --- [ main] o.m.e.web.config.ControllerConfig : Set max genes to 20 2021-06-18 11:24:55.996 INFO 228750 --- [ main] o.m.e.web.config.ControllerConfig : Instance is running in a NON-CLINICAL setting. 2021-06-18 11:24:56.005 WARN 228750 --- [ main] ConfigServletWebServerApplicationContext : Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'submitJobController': Unsatisfied dependency expressed through field 'exomiser'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiser' defined in URL [jar:file:/home/papachristos/projects/Exomiser/exomiser-web/target/exomiser-web-12.1.0.jar!/BOOT-INF/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/Exomiser.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisFactory' defined in URL [jar:file:/home/papachristos/projects/Exomiser/exomiser-web/target/exomiser-web-12.1.0.jar!/BOOT-INF/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisFactory.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.genome.GenomeAnalysisServiceProvider]: Factory method 'genomeAnalysisServiceProvider' threw exception; nested exception is java.lang.IllegalArgumentException: genomeAnalysisServices cannot be empty. 2021-06-18 11:24:56.008 INFO 228750 --- [ main] o.apache.catalina.core.StandardService : Stopping service [Tomcat] 2021-06-18 11:24:56.022 INFO 228750 --- [ main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled. 2021-06-18 11:24:56.025 ERROR 228750 --- [ main] o.s.boot.SpringApplication : Application run failed

org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'submitJobController': Unsatisfied dependency expressed through field 'exomiser'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiser' defined in URL [jar:file:/home/papachristos/projects/Exomiser/exomiser-web/target/exomiser-web-12.1.0.jar!/BOOT-INF/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/Exomiser.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisFactory' defined in URL [jar:file:/home/papachristos/projects/Exomiser/exomiser-web/target/exomiser-web-12.1.0.jar!/BOOT-INF/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisFactory.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.genome.GenomeAnalysisServiceProvider]: Factory method 'genomeAnalysisServiceProvider' threw exception; nested exception is java.lang.IllegalArgumentException: genomeAnalysisServices cannot be empty. at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:596) at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:90) at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessProperties(AutowiredAnnotationBeanPostProcessor.java:374) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1395) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:592) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:849) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:877) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:549) at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:142) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:775) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397) at org.springframework.boot.SpringApplication.run(SpringApplication.java:316) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1260) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1248) at org.monarchinitiative.exomiser.web.ExomiserWebApp.main(ExomiserWebApp.java:33) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48) at org.springframework.boot.loader.Launcher.launch(Launcher.java:87) at org.springframework.boot.loader.Launcher.launch(Launcher.java:50) at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:51) Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiser' defined in URL [jar:file:/home/papachristos/projects/Exomiser/exomiser-web/target/exomiser-web-12.1.0.jar!/BOOT-INF/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/Exomiser.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisFactory' defined in URL [jar:file:/home/papachristos/projects/Exomiser/exomiser-web/target/exomiser-web-12.1.0.jar!/BOOT-INF/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisFactory.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.genome.GenomeAnalysisServiceProvider]: Factory method 'genomeAnalysisServiceProvider' threw exception; nested exception is java.lang.IllegalArgumentException: genomeAnalysisServices cannot be empty. at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:769) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:218) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1325) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1171) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:277) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1247) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1167) at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:593) ... 27 common frames omitted Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisFactory' defined in URL [jar:file:/home/papachristos/projects/Exomiser/exomiser-web/target/exomiser-web-12.1.0.jar!/BOOT-INF/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisFactory.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.genome.GenomeAnalysisServiceProvider]: Factory method 'genomeAnalysisServiceProvider' threw exception; nested exception is java.lang.IllegalArgumentException: genomeAnalysisServices cannot be empty. at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:769) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:218) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1325) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1171) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:277) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1247) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1167) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:857) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:760) ... 40 common frames omitted Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.genome.GenomeAnalysisServiceProvider]: Factory method 'genomeAnalysisServiceProvider' threw exception; nested exception is java.lang.IllegalArgumentException: genomeAnalysisServices cannot be empty. at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:627) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:607) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1305) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1144) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:277) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1247) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1167) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:857) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:760) ... 54 common frames omitted Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.genome.GenomeAnalysisServiceProvider]: Factory method 'genomeAnalysisServiceProvider' threw exception; nested exception is java.lang.IllegalArgumentException: genomeAnalysisServices cannot be empty. at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:185) at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:622) ... 68 common frames omitted Caused by: java.lang.IllegalArgumentException: genomeAnalysisServices cannot be empty. at org.monarchinitiative.exomiser.core.genome.GenomeAnalysisServiceProvider.(GenomeAnalysisServiceProvider.java:41) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceAutoConfiguration.genomeAnalysisServiceProvider(GenomeAnalysisServiceAutoConfiguration.java:51) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$7300c41.CGLIB$genomeAnalysisServiceProvider$0() at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$7300c41$$FastClassBySpringCGLIB$$2829d134.invoke() at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:244) at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:363) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$7300c41.genomeAnalysisServiceProvider() at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:154) ... 69 common frames omitted

rejwan052 commented 3 years ago

Hi @stathispapachristos I'm facing the same problem when running the exomiser-web application. Can you solve this problem?

GreekByte commented 3 years ago

Hello @rejwan052! According to a colleague who knows Java, one needs to provide the following 3 parameters in the command: --exomiser.data-directory=/data/fast/exomizer/exomiser-cli-12.1.0/data/ --exomiser.hg19.data-version=2102 --exomiser.phenotype.data-version=2102