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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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Error running exsomiser: Error starting Application #439

Closed glustein closed 1 year ago

glustein commented 2 years ago

I am trying to run exomiser analysis using the test-analysis-exome.yml. It doesn´t works, I use the example provided by Exomiser, it produces this error:

java -Xms4g -Xmx8g -jar exomiser-cli-13.0.1.jar --analysis examples/test-analysis-exome.yml --spring.config.location=$HOME/bin/exomiser-cli-13.0.1/application.properties

java -Xms4g -Xmx8g -jar exomiser-cli-13.0.1.jar --analysis examples/test-analysis-exome.yml --spring.config.location=$HOME/bin/exomiser-cli-13.0.1/application.properties

Welcome to:

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A Tool to Annotate and Prioritize Exome Variants v13.0.1

2022-05-19 21:14:35.610 INFO 13980 --- [ main] org.monarchinitiative.exomiser.cli.Main : Starting Main using Java 11.0.15 on pop-os with PID 13980 (/home/glustein/bin/exomiser-cli-13.0.1/exomiser-cli-13.0.1.jar started by glustein in /home/glustein/bin/exomiser-cli-13.0.1) 2022-05-19 21:14:35.612 INFO 13980 --- [ main] org.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to default profiles: default 2022-05-19 21:14:36.059 INFO 13980 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /home/glustein/bin/exomiser-cli-13.0.1 2022-05-19 21:14:36.065 INFO 13980 --- [ main] o.m.exomiser.cli.config.MainConfig : Data source directory defined in properties as: data/exomiser-data 2022-05-19 21:14:36.065 INFO 13980 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /home/glustein/bin/exomiser-cli-13.0.1/data/exomiser-data 2022-05-19 21:14:36.068 INFO 13980 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /home/glustein/bin/exomiser-cli-13.0.1/data/exomiser-data/2109_hg19/2109_hg19_transcripts_ensembl.ser 2022-05-19 21:14:36.867 INFO 13980 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 0.797 sec. 2022-05-19 21:14:37.239 INFO 13980 --- [ main] o.m.e.c.g.dao.VariantWhiteListLoader : Loading variant whitelist from: /home/glustein/bin/exomiser-cli-13.0.1/data/exomiser-data/2109_hg19/2109_hg19_clinvar_whitelist.tsv.gz 2022-05-19 21:14:37.451 INFO 13980 --- [ main] o.m.e.c.g.dao.VariantWhiteListLoader : Loaded 112258 variants into whitelist 2022-05-19 21:14:38.584 ERROR 13980 --- [ main] com.zaxxer.hikari.pool.HikariPool : 2109_hg19_genome - Exception during pool initialization.

org.h2.jdbc.JdbcSQLNonTransientConnectionException: A file path that is implicitly relative to the current working directory is not allowed in the database URL "jdbc:h2:file:data/exomiser-data/2109_hg19/2109_hg19_genome;SCHEMA=exomiser;MODE=PostgreSQL;IFEXISTS=TRUE;AUTO_RECONNECT=TRUE;ACCESS_MODE_DATA=r;". Use an absolute path, ~/name, ./name, or the baseDir setting instead. [90011-200] at org.h2.message.DbException.getJdbcSQLException(DbException.java:622) at org.h2.message.DbException.getJdbcSQLException(DbException.java:429) at org.h2.message.DbException.get(DbException.java:205) at org.h2.message.DbException.get(DbException.java:181) at org.h2.engine.ConnectionInfo.getName(ConnectionInfo.java:396) at org.h2.engine.Engine.openSession(Engine.java:50) at org.h2.engine.Engine.openSession(Engine.java:192) at org.h2.engine.Engine.createSessionAndValidate(Engine.java:171) at org.h2.engine.Engine.createSession(Engine.java:166) at org.h2.engine.Engine.createSession(Engine.java:29) at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:340) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:173) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:152) at org.h2.Driver.connect(Driver.java:69) at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:138) at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:364) at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206) at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:476) at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:561) at com.zaxxer.hikari.pool.HikariPool.(HikariPool.java:115) at com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:112) at org.monarchinitiative.exomiser.core.genome.dao.RegulatoryFeatureDao.getRegulatoryFeatures(RegulatoryFeatureDao.java:57) at org.monarchinitiative.exomiser.core.genome.GenomeDataServiceImpl.getRegulatoryFeatures(GenomeDataServiceImpl.java:60) at org.monarchinitiative.exomiser.core.genome.GenomeDataService.getRegulatoryRegionIndex(GenomeDataService.java:40) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.buildVariantAnnotator(GenomeAnalysisServiceConfigurer.java:71) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration.variantAnnotator(Hg19GenomeAnalysisServiceAutoConfiguration.java:77) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5.CGLIB$variantAnnotator$2() at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5$$FastClassBySpringCGLIB$$d49ea69b.invoke() at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:244) at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:331) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5.variantAnnotator() 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:566) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:154) at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:653) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:486) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1334) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1177) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.resolveBeanReference(ConfigurationClassEnhancer.java:362) at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:334) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5.variantAnnotator() at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.buildGenomeAnalysisService(GenomeAnalysisServiceConfigurer.java:102) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration.genomeAnalysisService(Hg19GenomeAnalysisServiceAutoConfiguration.java:102) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5.CGLIB$genomeAnalysisService$0() at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5$$FastClassBySpringCGLIB$$d49ea69b.invoke() at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:244) at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:331) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5.genomeAnalysisService() 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:566) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:154) at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:653) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:486) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1334) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1177) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276) at org.springframework.beans.factory.support.DefaultListableBeanFactory.addCandidateEntry(DefaultListableBeanFactory.java:1598) at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1562) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveMultipleBeans(DefaultListableBeanFactory.java:1428) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1338) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1300) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:541) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1334) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1177) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1380) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1300) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:229) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1354) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1204) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1380) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1300) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:229) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1354) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1204) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1380) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1300) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:229) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1354) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1204) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:944) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:583) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:754) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:434) at org.springframework.boot.SpringApplication.run(SpringApplication.java:338) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332) at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53)

2022-05-19 21:14:38.586 ERROR 13980 --- [ main] o.m.e.c.genome.dao.RegulatoryFeatureDao : Error executing regulatory feature query:

org.h2.jdbc.JdbcSQLNonTransientConnectionException: A file path that is implicitly relative to the current working directory is not allowed in the database URL "jdbc:h2:file:data/exomiser-data/2109_hg19/2109_hg19_genome;SCHEMA=exomiser;MODE=PostgreSQL;IFEXISTS=TRUE;AUTO_RECONNECT=TRUE;ACCESS_MODE_DATA=r;". Use an absolute path, ~/name, ./name, or the baseDir setting instead. [90011-200] at org.h2.message.DbException.getJdbcSQLException(DbException.java:622) at org.h2.message.DbException.getJdbcSQLException(DbException.java:429) at org.h2.message.DbException.get(DbException.java:205) at org.h2.message.DbException.get(DbException.java:181) at org.h2.engine.ConnectionInfo.getName(ConnectionInfo.java:396) at org.h2.engine.Engine.openSession(Engine.java:50) at org.h2.engine.Engine.openSession(Engine.java:192) at org.h2.engine.Engine.createSessionAndValidate(Engine.java:171) at org.h2.engine.Engine.createSession(Engine.java:166) at org.h2.engine.Engine.createSession(Engine.java:29) at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:340) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:173) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:152) at org.h2.Driver.connect(Driver.java:69) at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:138) at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:364) at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206) at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:476) at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:561) at com.zaxxer.hikari.pool.HikariPool.(HikariPool.java:115) at com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:112) at org.monarchinitiative.exomiser.core.genome.dao.RegulatoryFeatureDao.getRegulatoryFeatures(RegulatoryFeatureDao.java:57) at org.monarchinitiative.exomiser.core.genome.GenomeDataServiceImpl.getRegulatoryFeatures(GenomeDataServiceImpl.java:60) at org.monarchinitiative.exomiser.core.genome.GenomeDataService.getRegulatoryRegionIndex(GenomeDataService.java:40) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.buildVariantAnnotator(GenomeAnalysisServiceConfigurer.java:71) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration.variantAnnotator(Hg19GenomeAnalysisServiceAutoConfiguration.java:77) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5.CGLIB$variantAnnotator$2() at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5$$FastClassBySpringCGLIB$$d49ea69b.invoke() at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:244) at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:331) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5.variantAnnotator() 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:566) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:154) at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:653) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:486) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1334) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1177) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.resolveBeanReference(ConfigurationClassEnhancer.java:362) at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:334) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5.variantAnnotator() at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.buildGenomeAnalysisService(GenomeAnalysisServiceConfigurer.java:102) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration.genomeAnalysisService(Hg19GenomeAnalysisServiceAutoConfiguration.java:102) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5.CGLIB$genomeAnalysisService$0() at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5$$FastClassBySpringCGLIB$$d49ea69b.invoke() at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:244) at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:331) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$9833ced5.genomeAnalysisService() 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:566) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:154) at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:653) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:486) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1334) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1177) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276) at org.springframework.beans.factory.support.DefaultListableBeanFactory.addCandidateEntry(DefaultListableBeanFactory.java:1598) at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1562) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveMultipleBeans(DefaultListableBeanFactory.java:1428) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1338) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1300) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:541) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1334) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1177) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1380) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1300) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:229) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1354) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1204) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1380) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1300) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:229) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1354) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1204) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1380) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1300) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:229) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1354) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1204) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:564) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:944) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:583) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:754) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:434) at org.springframework.boot.SpringApplication.run(SpringApplication.java:338) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332) at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53)

2022-05-19 21:14:38.596 INFO 13980 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /home/glustein/bin/exomiser-cli-13.0.1/data/exomiser-data/2109_hg38/2109_hg38_transcripts_ensembl.ser ^Z [8] + 13980 suspended java -Xms4g -Xmx8g -jar exomiser-cli-13.0.1.jar --analysis 

at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:83)
at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:69)
at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJob(ExomiserCommandLineRunner.java:79)
at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJobs(ExomiserCommandLineRunner.java:62)
at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.run(ExomiserCommandLineRunner.java:57)
at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:791)
at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:775)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:345)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332)
at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53)

2022-05-19 21:10:34.851 ERROR 13512 --- [ main] o.m.e.c.p.dao.DefaultDiseaseDao : Unable to execute query 'SELECT gene_id AS entrez_id, symbol AS human_gene_symbol, d.disease_id AS disease_id, d.diseasename AS disease_name, d.type AS disease_type, d.inheritance AS inheritance_code, hp_id AS pheno_ids FROM entrez2sym e, disease_hp dhp, disease d WHERE dhp.disease_id = d.disease_id AND e.entrezid = d.gene_id AND d.type in ('D', 'C', 'S', '?')AND d.gene_id = ?' for geneId: '51398'

org.h2.jdbc.JdbcSQLNonTransientConnectionException: A file path that is implicitly relative to the current working directory is not allowed in the database URL "jdbc:h2:file:data/exomiser-data/2109_phenotype/2109_phenotype;SCHEMA=exomiser;MODE=PostgreSQL;IFEXISTS=TRUE;AUTO_RECONNECT=TRUE;ACCESS_MODE_DATA=r;". Use an absolute path, ~/name, ./name, or the baseDir setting instead. [90011-200] at org.h2.message.DbException.getJdbcSQLException(DbException.java:622) at org.h2.message.DbException.getJdbcSQLException(DbException.java:429) at org.h2.message.DbException.get(DbException.java:205) at org.h2.message.DbException.get(DbException.java:181) at org.h2.engine.ConnectionInfo.getName(ConnectionInfo.java:396) at org.h2.engine.Engine.openSession(Engine.java:50) at org.h2.engine.Engine.openSession(Engine.java:192) at org.h2.engine.Engine.createSessionAndValidate(Engine.java:171) at org.h2.engine.Engine.createSession(Engine.java:166) at org.h2.engine.Engine.createSession(Engine.java:29) at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:340) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:173) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:152) at org.h2.Driver.connect(Driver.java:69) at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:138) at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:364) at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206) at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:476) at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:561) at com.zaxxer.hikari.pool.HikariPool.(HikariPool.java:115) at com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:112) at org.monarchinitiative.exomiser.core.prioritisers.dao.DefaultDiseaseDao.getDiseaseDataAssociatedWithGeneId(DefaultDiseaseDao.java:104) at org.monarchinitiative.exomiser.core.prioritisers.dao.DefaultDiseaseDao$$FastClassBySpringCGLIB$$376ec0c7.invoke() at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:779) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:137) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) at org.springframework.cache.interceptor.CacheInterceptor.lambda$invoke$0(CacheInterceptor.java:54) at org.springframework.cache.interceptor.CacheAspectSupport.invokeOperation(CacheAspectSupport.java:366) at org.springframework.cache.interceptor.CacheAspectSupport.execute(CacheAspectSupport.java:421) at org.springframework.cache.interceptor.CacheAspectSupport.execute(CacheAspectSupport.java:345) at org.springframework.cache.interceptor.CacheInterceptor.invoke(CacheInterceptor.java:64) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:692) at org.monarchinitiative.exomiser.core.prioritisers.dao.DefaultDiseaseDao$$EnhancerBySpringCGLIB$$2f1f4ce8.getDiseaseDataAssociatedWithGeneId() at org.monarchinitiative.exomiser.core.prioritisers.service.PriorityService.getDiseaseDataAssociatedWithGeneId(PriorityService.java:106) at org.monarchinitiative.exomiser.core.prioritisers.service.PriorityService$$FastClassBySpringCGLIB$$a299cac4.invoke() at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:688) at org.monarchinitiative.exomiser.core.prioritisers.service.PriorityService$$EnhancerBySpringCGLIB$$1c0410ff.getDiseaseDataAssociatedWithGeneId() at org.monarchinitiative.exomiser.core.prioritisers.OmimPriority.lambda$prioritiseGene$0(OmimPriority.java:91) at org.monarchinitiative.exomiser.core.prioritisers.OmimPriority.prioritizeGenes(OmimPriority.java:73) at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.runStep(AbstractAnalysisRunner.java:340) at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.runSteps(AbstractAnalysisRunner.java:304) at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.run(AbstractAnalysisRunner.java:119) at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:83) at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:69) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJob(ExomiserCommandLineRunner.java:79) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJobs(ExomiserCommandLineRunner.java:62) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.run(ExomiserCommandLineRunner.java:57) at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:791) at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:775) at org.springframework.boot.SpringApplication.run(SpringApplication.java:345) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332) at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53)

2022-05-19 21:10:35.852 ERROR 13512 --- [ main] com.zaxxer.hikari.pool.HikariPool : 2109_phenotype - Exception during pool initialization.

org.h2.jdbc.JdbcSQLNonTransientConnectionException: A file path that is implicitly relative to the current working directory is not allowed in the database URL "jdbc:h2:file:data/exomiser-data/2109_phenotype/2109_phenotype;SCHEMA=exomiser;MODE=PostgreSQL;IFEXISTS=TRUE;AUTO_RECONNECT=TRUE;ACCESS_MODE_DATA=r;". Use an absolute path, ~/name, ./name, or the baseDir setting instead. [90011-200] at org.h2.message.DbException.getJdbcSQLException(DbException.java:622) at org.h2.message.DbException.getJdbcSQLException(DbException.java:429) at org.h2.message.DbException.get(DbException.java:205) at org.h2.message.DbException.get(DbException.java:181) at org.h2.engine.ConnectionInfo.getName(ConnectionInfo.java:396) at org.h2.engine.Engine.openSession(Engine.java:50) at org.h2.engine.Engine.openSession(Engine.java:192)

2022-05-19 21:12:01.381 ERROR 13512 --- [ main] o.m.e.c.p.dao.DefaultDiseaseDao : Unable to execute query 'SELECT gene_id AS entrez_id, symbol AS human_gene_symbol, d.disease_id AS disease_id, d.diseasename AS disease_name, d.type AS disease_type, d.inheritance AS inheritance_code, hp_id AS pheno_ids FROM entrez2sym e, disease_hp dhp, disease d WHERE dhp.disease_id = d.disease_id AND e.entrezid = d.gene_id AND d.type in ('D', 'C', 'S', '?')AND d.gene_id = ?' for geneId: '93611'

org.h2.jdbc.JdbcSQLNonTransientConnectionException: A file path that is implicitly relative to the current working directory is not allowed in the database URL "jdbc:h2:file:data/exomiser-data/2109_phenotype/2109_phenotype;SCHEMA=exomiser;MODE=PostgreSQL;IFEXISTS=TRUE;AUTO_RECONNECT=TRUE;ACCESS_MODE_DATA=r;". Use an absolute path, ~/name, ./name, or the baseDir setting instead. [90011-200] at org.h2.message.DbException.getJdbcSQLException(DbException.java:622) at org.h2.message.DbException.getJdbcSQLException(DbException.java:429) at org.h2.message.DbException.get(DbException.java:205) at org.h2.message.DbException.get(DbException.java:181) at org.h2.engine.ConnectionInfo.getName(ConnectionInfo.java:396) at org.h2.engine.Engine.openSession(Engine.java:50) at org.h2.engine.Engine.openSession(Engine.java:192) at org.h2.engine.Engine.createSessionAndValidate(Engine.java:171) at org.h2.engine.Engine.createSession(Engine.java:166) at org.h2.engine.Engine.createSession(Engine.java:29) at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:340) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:173) at org.h2.jdbc.JdbcConnection.(JdbcConnection.java:152) at org.h2.Driver.connect(Driver.java:69) at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:138) at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:364) at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206) at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:476) at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:561) at com.zaxxer.hikari.pool.HikariPool.(HikariPool.java:115) at com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:112) at org.monarchinitiative.exomiser.core.prioritisers.dao.DefaultDiseaseDao.getDiseaseDataAssociatedWithGeneId(DefaultDiseaseDao.java:104) at org.monarchinitiative.exomiser.core.prioritisers.dao.DefaultDiseaseDao$$FastClassBySpringCGLIB$$376ec0c7.invoke() at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:779) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:137) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) at org.springframework.cache.interceptor.CacheInterceptor.lambda$invoke$0(CacheInterceptor.java:54) at org.springframework.cache.interceptor.CacheAspectSupport.invokeOperation(CacheAspectSupport.java:366) at org.springframework.cache.interceptor.CacheAspectSupport.execute(CacheAspectSupport.java:421) at org.springframework.cache.interceptor.CacheAspectSupport.execute(CacheAspectSupport.java:345) at org.springframework.cache.interceptor.CacheInterceptor.invoke(CacheInterceptor.java:64) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:692) at org.monarchinitiative.exomiser.core.prioritisers.dao.DefaultDiseaseDao$$EnhancerBySpringCGLIB$$2f1f4ce8.getDiseaseDataAssociatedWithGeneId() at org.monarchinitiative.exomiser.core.prioritisers.service.PriorityService.getDiseaseDataAssociatedWithGeneId(PriorityService.java:106) at org.monarchinitiative.exomiser.core.prioritisers.service.PriorityService$$FastClassBySpringCGLIB$$a299cac4.invoke() at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:688) at org.monarchinitiative.exomiser.core.prioritisers.service.PriorityService$$EnhancerBySpringCGLIB$$1c0410ff.getDiseaseDataAssociatedWithGeneId() at org.monarchinitiative.exomiser.core.prioritisers.OmimPriority.lambda$prioritiseGene$0(OmimPriority.java:91) at org.monarchinitiative.exomiser.core.prioritisers.OmimPriority.prioritizeGenes(OmimPriority.java:73) at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.runStep(AbstractAnalysisRunner.java:340) at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.runSteps(AbstractAnalysisRunner.java:304) at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.run(AbstractAnalysisRunner.java:119) at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:83) at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:69) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJob(ExomiserCommandLineRunner.java:79) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJobs(ExomiserCommandLineRunner.java:62) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.run(ExomiserCommandLineRunner.java:57) at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:791) at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:775) at org.springframework.boot.SpringApplication.run(SpringApplication.java:345) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332) at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53)

2022-05-19 21:12:02.383 ERROR 13512 --- [ main] com.zaxxer.hikari.pool.HikariPool : 2109_phenotype - Exception during pool initialization.

org.h2.jdbc.JdbcSQLNonTransientConnectionException: A file path that is implicitly relative to the current working directory is not allowed in the database URL "jdbc:h2:file:data/exomiser-data/2109_phenotype/2109_phenotype;SCHEMA=exomiser;MODE=PostgreSQL;IFEXISTS=TRUE;AUTO_RECONNECT=TRUE;ACCESS_MODE_DATA=r;". Use an absolute path, ~/name, ./name, or the baseDir setting instead. [90011-200] at org.h2.message.DbException.getJdbcSQLException(DbException.java:622) at org.h2.message.DbException.getJdbcSQLException(DbException.java:429) at org.h2.message.DbException.get(DbException.java:205) at org.h2.message.DbException.get(DbException.java:181) at org.h2.engine.ConnectionInfo.getName(ConnectionInfo.java:396) at org.h2.engine.Engine.openSession(Engine.java:50) at org.h2.engine.Engine.openSession(Engine.java:192) at org.h2.engine.Engine.createSessionAndValidate(Engine.java:171) at org.h2.engine.Engine.createSession(Engine.java:166) at org.h2.engine.Engine.createSession(Engine.java:29) at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:340)

This it is repited againt and againt...

Can someone help me with this error ? Thank you

ielis commented 2 years ago

Hello @glustein I think the following line is the culprit:

org.h2.jdbc.JdbcSQLNonTransientConnectionException: A file path that is implicitly relative to the current working directory is not allowed in the database URL "jdbc:h2:file:data/exomiser-data/2109_phenotype/2109_phenotype;SCHEMA=exomiser;MODE=PostgreSQL;IFEXISTS=TRUE;AUTO_RECONNECT=TRUE;ACCESS_MODE_DATA=r;". Use an absolute path, ~/name, ./name, or the baseDir setting instead. [90011-200]

Based on the line, you should set an absolute path to exomiser.data-directory property in your application.properties file. That's the 1st thing I would try.