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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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Test genome analysis failed on exomiser 11 #346

Closed Wanda-Sankey closed 5 years ago

Wanda-Sankey commented 5 years ago

I tried running the test genomiser analysis using:

java -Xms4g -Xmx8g -jar exomiser-cli-11.0.0.jar --analysis test-analysis-genome.yml

I get the error:

A Tool to Annotate and Prioritize Exome Variants v11.0.0

2019-09-12 14:45:40.983 INFO 26100 --- [ main] org.monarchinitiative.exomiser.cli.Main : Starting Main on FVFYXE28L410 with PID 26100 (started by Wanda.Sankey in /Users/Wanda.Sankey/Documents/Software Support/exomiser-cli-11.0.0) 2019-09-12 14:45:40.985 INFO 26100 --- [ main] org.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to default profiles: default 2019-09-12 14:45:41.020 INFO 26100 --- [ main] s.c.a.AnnotationConfigApplicationContext : Refreshing org.springframework.context.annotation.AnnotationConfigApplicationContext@15aab8c6: startup date [Thu Sep 12 14:45:41 EDT 2019]; root of context hierarchy WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.springframework.cglib.core.ReflectUtils$1 (file:/Users/Wanda.Sankey/Documents/Software%20Support/exomiser-cli-11.0.0/lib/spring-core-5.0.8.RELEASE.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) WARNING: Please consider reporting this to the maintainers of org.springframework.cglib.core.ReflectUtils$1 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release 2019-09-12 14:45:41.774 INFO 26100 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /Users/Wanda.Sankey/Documents/Software Support/exomiser-cli-11.0.0 2019-09-12 14:45:41.787 INFO 26100 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser data directory not defined in properties. Checking for default... 2019-09-12 14:45:41.787 INFO 26100 --- [ main] o.m.exomiser.cli.config.MainConfig : Found default data directory: /Users/Wanda.Sankey/Documents/Software Support/exomiser-cli-11.0.0/data 2019-09-12 14:45:41.802 INFO 26100 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Starting... 2019-09-12 14:45:42.020 INFO 26100 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Start completed. 2019-09-12 14:45:46.322 INFO 26100 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-genome-hg19-1811 - Starting... 2019-09-12 14:45:47.335 ERROR 26100 --- [ main] com.zaxxer.hikari.pool.HikariPool : exomiser-genome-hg19-1811 - Exception during pool initialization.

org.h2.jdbc.JdbcSQLException: Database "/Users/Wanda.Sankey/Documents/Software Support/exomiser-cli-11.0.0/${exomiser.data-directory}/1811_hg19/1811_hg19_genome" not found [90013-197] at org.h2.message.DbException.getJdbcSQLException(DbException.java:357) at org.h2.message.DbException.get(DbException.java:179) at org.h2.message.DbException.get(DbException.java:155) at org.h2.engine.Engine.openSession(Engine.java:64) at org.h2.engine.Engine.openSession(Engine.java:179) at org.h2.engine.Engine.createSessionAndValidate(Engine.java:157) at org.h2.engine.Engine.createSession(Engine.java:140) at org.h2.engine.Engine.createSession(Engine.java:28) at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:351) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:124) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:103) at org.h2.Driver.connect(Driver.java:69) at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:117) at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:123) at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:365) at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:194) at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:460) at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:534) at com.zaxxer.hikari.pool.HikariPool.(HikariPool.java:115) at com.zaxxer.hikari.HikariDataSource.(HikariDataSource.java:81) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeDataSources.buildGenomeDataSource(GenomeDataSources.java:119) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeDataSources.from(GenomeDataSources.java:72) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.(GenomeAnalysisServiceConfigurer.java:65) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration.(Hg19GenomeAnalysisServiceAutoConfiguration.java:46) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9077ad76.() at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:481) at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:170) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:117) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:275) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1267) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1124) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:535) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:495) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:317) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:315) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:372) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1247) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1096) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:535) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:495) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:317) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:315) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:251) at org.springframework.beans.factory.support.DefaultListableBeanFactory.addCandidateEntry(DefaultListableBeanFactory.java:1322) at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1288) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveMultipleBeans(DefaultListableBeanFactory.java:1170) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1093) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1062) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:818) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:724) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:474) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1247) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1096) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:535) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:495) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:317) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:315) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:251) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1135) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1062) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:818) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:724) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:197) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1267) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1124) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:535) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:495) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:317) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:315) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:251) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1135) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1062) at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:583) at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:91) at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:372) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1341) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:572) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:495) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:317) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:315) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:759) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:869) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:550) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:762) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:398) at org.springframework.boot.SpringApplication.run(SpringApplication.java:330) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1258) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1246) at org.monarchinitiative.exomiser.cli.Main.main(Main.java:44)

2019-09-12 14:45:47.339 WARN 26100 --- [ main] s.c.a.AnnotationConfigApplicationContext : Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiserCommandLineRunner': Unsatisfied dependency expressed through field 'analysisParser'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisParser' defined in URL [jar:file:/Users/Wanda.Sankey/Documents/Software%20Support/exomiser-cli-11.0.0/lib/exomiser-core-11.0.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisParser.class]: Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Unsatisfied dependency expressed through method 'genomeAnalysisServiceProvider' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration': Bean instantiation via constructor failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9077ad76]: Constructor threw exception; nested exception is com.zaxxer.hikari.pool.HikariPool$PoolInitializationException: Failed to initialize pool: Database "/Users/Wanda.Sankey/Documents/Software Support/exomiser-cli-11.0.0/${exomiser.data-directory}/1811_hg19/1811_hg19_genome" not found [90013-197] 2019-09-12 14:45:47.342 INFO 26100 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Shutdown initiated... 2019-09-12 14:45:47.349 INFO 26100 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Shutdown completed.

Wanda-Sankey commented 5 years ago

I realized I uncommented the line:

exomiser.hg19.data-directory=${exomiser.data-directory}/${exomiser.hg19.data-version}_hg19

in application.properties, it seems to no longer have the error now!