julesjacobsen
commented
3 years ago Have you downloaded the data?
The error says it can't find the file "/Users/admin/exomiser-cli-12.1.0/data/1902_hg19/1902_hg19_genome"
If you have downloaded the data you'll need to edit the application.properties file to point to the data directories. The data can be found at https://data.monarchinitiative.org/exomiser/latest/. You'll need to select at least one of the genome assemblies and the phenotype data. Unzip them to an exomiser-data directory and then add the full path to this in the application.properties file. For example, if you have downloaded and extracted the 2102_hg19.zip and 2102_phenotype.zip data to /data/exomiser-data , you'll need to edit the application.properties file to point to the correct root data directory and the current data versions like this:
#root path where data is to be downloaded and worked on
#it is assumed that all the files required by exomiser listed in this properties file
#will be found in the data directory unless specifically overridden here.
exomiser.data-directory=/data/exomiser-data
### hg19 assembly ###
exomiser.hg19.data-version=2102
### hg38 assembly ###
# To enable analysis of samples called against the hg38 assembly copy the hg19 above and just replace the hg19 with hg38
# exomiser.hg38.data-version=2102
### phenotypes ###
exomiser.phenotype.data-version=2102Should get you up and running. It is important to keep these data up to date as you'll miss newly discovered gene-disease associations if you don't.
NoorUlAyan
GayatriNavle
2021-02-10 11:14:27.809 WARN 6157 --- [ 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/admin/exomiser-cli-12.1.0/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisParser.class]: Unsatisfied dependency expressed through constructor parameter 0; 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$$EnhancerBySpringCGLIB$$af7fb501]: Constructor threw exception; nested exception is com.zaxxer.hikari.pool.HikariPool$PoolInitializationException: Failed to initialize pool: Database "/Users/admin/exomiser-cli-12.1.0/data/1902_hg19/1902_hg19_genome" not found [90013-197] 2021-02-10 11:14:27.816 INFO 6157 --- [ main] ConditionEvaluationReportLoggingListener :
Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled. 2021-02-10 11:14:27.817 ERROR 6157 --- [ main] o.s.boot.SpringApplication : Application run failed
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/admin/exomiser-cli-12.1.0/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisParser.class]: Unsatisfied dependency expressed through constructor parameter 0; 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$$EnhancerBySpringCGLIB$$af7fb501]: Constructor threw exception; nested exception is com.zaxxer.hikari.pool.HikariPool$PoolInitializationException: Failed to initialize pool: Database "/Users/admin/exomiser-cli-12.1.0/data/1902_hg19/1902_hg19_genome" not found [90013-197] at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$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.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.cli.Main.main(Main.java:44) Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisParser' defined in URL [jar:file:/Users/admin/exomiser-cli-12.1.0/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisParser.class]: Unsatisfied dependency expressed through constructor parameter 0; 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$$EnhancerBySpringCGLIB$$af7fb501]: Constructor threw exception; nested exception is com.zaxxer.hikari.pool.HikariPool$PoolInitializationException: Failed to initialize pool: Database "/Users/admin/exomiser-cli-12.1.0/data/1902_hg19/1902_hg19_genome" not found [90013-197] at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:769) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:218) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1325) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1171) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$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) ... 18 common frames omitted Caused by: 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$$EnhancerBySpringCGLIB$$af7fb501]: Constructor threw exception; nested exception is com.zaxxer.hikari.pool.HikariPool$PoolInitializationException: Failed to initialize pool: Database "/Users/admin/exomiser-cli-12.1.0/data/1902_hg19/1902_hg19_genome" not found [90013-197] at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:769) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:509) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1305) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1144) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$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) ... 31 common frames omitted Caused by: 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$$EnhancerBySpringCGLIB$$af7fb501]: Constructor threw exception; nested exception is com.zaxxer.hikari.pool.HikariPool$PoolInitializationException: Failed to initialize pool: Database "/Users/admin/exomiser-cli-12.1.0/data/1902_hg19/1902_hg19_genome" not found [90013-197] at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:304) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1325) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1171) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:392) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1305) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1144) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$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.addCandidateEntry(DefaultListableBeanFactory.java:1463) at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1427) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveMultipleBeans(DefaultListableBeanFactory.java:1295) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1205) 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) ... 45 common frames omitted Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$af7fb501]: Constructor threw exception; nested exception is com.zaxxer.hikari.pool.HikariPool$PoolInitializationException: Failed to initialize pool: Database "/Users/admin/exomiser-cli-12.1.0/data/1902_hg19/1902_hg19_genome" not found [90013-197] at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:184) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:117) at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:300) ... 71 common frames omitted Caused by: com.zaxxer.hikari.pool.HikariPool$PoolInitializationException: Failed to initialize pool: Database "/Users/admin/exomiser-cli-12.1.0/data/1902_hg19/1902_hg19_genome" not found [90013-197] at com.zaxxer.hikari.pool.HikariPool.throwPoolInitializationException(HikariPool.java:576) at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:562) 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:129)
at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeDataSources.from(GenomeDataSources.java:76)
at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.(GenomeAnalysisServiceConfigurer.java:68)
at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration.(Hg19GenomeAnalysisServiceAutoConfiguration.java:46)
at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$af7fb501.()
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:64)
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:172)
... 73 common frames omitted
Caused by: org.h2.jdbc.JdbcSQLException: Database "/Users/admin/exomiser-cli-12.1.0/data/1902_hg19/1902_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:136)
at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:369)
at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:198)
at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:467)
at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:541)
... 86 common frames omitted