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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
202 stars 55 forks source link

test exome analysis failed for exomiser version 9.0.1 #245

Closed hongenxu closed 6 years ago

hongenxu commented 6 years ago

My linux is centOS 7, I ran

java -jar exomiser-cli-9.0.1.jar --analysis examples/test-analysis-exome.yml

got the errors as follows

A Tool to Annotate and Prioritize Exome Variants     v9.0.1

2018-02-02 10:12:45.724 [main] INFO  org.monarchinitiative.exomiser.cli.Main - Starting Main on mu02 with PID 62335 (/public/home/pmc1/src/exomiser-cli-9.0.1/exomiser-cli-9.0.1.jar started by pmc1 in /public/home/pmc1/src/exomiser-cli-9.0.1)
2018-02-02 10:12:45.724 [main] INFO  org.monarchinitiative.exomiser.cli.Main - No active profile set, falling back to default profiles: default
2018-02-02 10:12:45.766 [main] INFO  org.springframework.context.annotation.AnnotationConfigApplicationContext - Refreshing org.springframework.context.annotation.AnnotationConfigApplicationContext@1b84f475: startup date [Fri Feb 02 10:12:45 CST 2018]; root of context hierarchy
2018-02-02 10:12:46.210 [main] INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'settingsParser' with a different definition: replacing [Generic bean: class [org.monarchinitiative.exomiser.core.analysis.SettingsParser]; scope=singleton; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [jar:file:/public/home/pmc1/src/exomiser-cli-9.0.1/lib/exomiser-core-9.0.1.jar!/org/monarchinitiative/exomiser/core/analysis/SettingsParser.class]] with [Root bean: class [null]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfiguration; factoryMethodName=settingsParser; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/ExomiserAutoConfiguration.class]]
2018-02-02 10:12:46.594 [main] INFO  org.monarchinitiative.exomiser.cli.config.MainConfig - Exomiser home: /public/home/pmc1/src/exomiser-cli-9.0.1
2018-02-02 10:12:46.599 [main] INFO  org.monarchinitiative.exomiser.cli.config.MainConfig - Data source directory defined in properties as: data
2018-02-02 10:12:46.599 [main] INFO  org.monarchinitiative.exomiser.cli.config.MainConfig - Root data source directory set to: /public/home/pmc1/src/exomiser-cli-9.0.1/data
2018-02-02 10:12:46.600 [main] INFO  org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer - Configuring hg19 assembly (data-version=1711, transcript-source=ensembl)
2018-02-02 10:12:46.618 [main] INFO  org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer - Using ensembl transcript source for hg19
2018-02-02 10:12:46.619 [main] INFO  de.charite.compbio.jannovar.data.JannovarDataSerializer - Deserializing JannovarData from /public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_transcripts_ensembl.ser
2018-02-02 10:14:49.156 [main] INFO  de.charite.compbio.jannovar.data.JannovarDataSerializer - Deserialization took 122.53 sec.
2018-02-02 10:14:49.163 [main] INFO  com.zaxxer.hikari.HikariDataSource - exomiser-genome-hg19-1711 - Started.
2018-02-02 10:14:49.347 [main] INFO  org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer - Opening MVStore from /public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db
2018-02-02 10:14:49.359 [main] WARN  org.springframework.context.annotation.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:/public/home/pmc1/src/exomiser-cli-9.0.1/lib/exomiser-core-9.0.1.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$$EnhancerBySpringCGLIB$$5f23d27d]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1]
2018-02-02 10:14:49.367 [main] INFO  org.springframework.boot.autoconfigure.logging.AutoConfigurationReportLoggingInitializer -

Error starting ApplicationContext. To display the auto-configuration report re-run your application with 'debug' enabled.
2018-02-02 10:14:49.371 [main] ERROR org.springframework.boot.SpringApplication - Application startup 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:/public/home/pmc1/src/exomiser-cli-9.0.1/lib/exomiser-core-9.0.1.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$$EnhancerBySpringCGLIB$$5f23d27d]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1]
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:588)
        at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:88)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:366)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1264)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
        at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:693)
        at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:360)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:303)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1118)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1107)
        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:/public/home/pmc1/src/exomiser-cli-9.0.1/lib/exomiser-core-9.0.1.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$$EnhancerBySpringCGLIB$$5f23d27d]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1]
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1193)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1095)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:585)
        ... 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$$EnhancerBySpringCGLIB$$5f23d27d]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1]
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
        at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:467)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1173)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1067)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835)
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741)
        ... 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$$EnhancerBySpringCGLIB$$5f23d27d]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1]
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:279)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1193)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1095)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
        at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:372)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1173)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1067)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.addCandidateEntry(DefaultListableBeanFactory.java:1316)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1282)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveMultipleBeans(DefaultListableBeanFactory.java:1160)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1096)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835)
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741)
        ... 45 common frames omitted
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$5f23d27d]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1]
        at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:154)
        at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:122)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:271)
        ... 70 common frames omitted
Caused by: java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1]
        at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:765)
        at org.h2.mvstore.FileStore.open(FileStore.java:179)
        at org.h2.mvstore.MVStore.<init>(MVStore.java:347)
        at org.h2.mvstore.MVStore$Builder.open(MVStore.java:2930)
        at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.openMvStore(GenomeAnalysisServiceConfigurer.java:212)
        at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.<init>(GenomeAnalysisServiceConfigurer.java:67)
        at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration.<init>(Hg19GenomeAnalysisServiceAutoConfiguration.java:44)
        at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$5f23d27d.<init>(<generated>)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
        at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:142)
        ... 72 common frames omitted
Caused by: java.io.IOException: Function not implemented
        at sun.nio.ch.FileDispatcherImpl.lock0(Native Method)
        at sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:90)
        at sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1115)
        at org.h2.store.fs.FileNio.tryLock(FilePathNio.java:121)
        at org.h2.mvstore.FileStore.open(FileStore.java:163)
        ... 83 common frames omitted
julesjacobsen commented 6 years ago

Does the file /public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db exist?

If it does it might be corrupted and you could try extracting it again or re-downloading and extracting once more.

hongenxu commented 6 years ago

thanks for your reply. I re-downloaded the data files, unzipped, got the errors,

A Tool to Annotate and Prioritize Exome Variants v9.0.1

2018-02-04 17:59:46.324 [main] INFO org.monarchinitiative.exomiser.cli.Main - Starting Main on mu02 with PID 25330 (/public/home/pmc1/src/exomiser-cli-9.0.1/exomiser-cli-9.0.1.jar started by pmc1 in /public/home/pmc1/src/exomiser-cli-9.0.1) 2018-02-04 17:59:46.325 [main] INFO org.monarchinitiative.exomiser.cli.Main - No active profile set, falling back to default profiles: default 2018-02-04 17:59:46.366 [main] INFO org.springframework.context.annotation.AnnotationConfigApplicationContext - Refreshing org.springframework.context.annotation.AnnotationConfigApplicationContext@1b84f475: startup date [Sun Feb 04 17:59:46 CST 2018]; root of context hierarchy 2018-02-04 17:59:52.793 [main] INFO org.springframework.beans.factory.support.DefaultListableBeanFactory - Overriding bean definition for bean 'settingsParser' with a different definition: replacing [Generic bean: class [org.monarchinitiative.exomiser.core.analysis.SettingsParser]; scope=singleton; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [jar:file:/public/home/pmc1/src/exomiser-cli-9.0.1/lib/exomiser-core-9.0.1.jar!/org/monarchinitiative/exomiser/core/analysis/SettingsParser.class]] with [Root bean: class [null]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfiguration; factoryMethodName=settingsParser; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/ExomiserAutoConfiguration.class]] 2018-02-04 17:59:53.279 [main] INFO org.monarchinitiative.exomiser.cli.config.MainConfig - Exomiser home: /public/home/pmc1/src/exomiser-cli-9.0.1 2018-02-04 17:59:53.296 [main] INFO org.monarchinitiative.exomiser.cli.config.MainConfig - Exomiser data directory not defined in properties. Checking for default... 2018-02-04 17:59:53.297 [main] INFO org.monarchinitiative.exomiser.cli.config.MainConfig - Found default data directory: /public/home/pmc1/src/exomiser-cli-9.0.1/data 2018-02-04 17:59:53.323 [main] INFO org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer - Configuring hg19 assembly (data-version=1711, transcript-source=ucsc) 2018-02-04 17:59:53.324 [main] INFO org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer - Using ucsc transcript source for hg19 2018-02-04 17:59:53.328 [main] INFO de.charite.compbio.jannovar.data.JannovarDataSerializer - Deserializing JannovarData from /public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_transcripts_ucsc.ser 2018-02-04 18:02:05.755 [main] INFO de.charite.compbio.jannovar.data.JannovarDataSerializer - Deserialization took 132.42 sec. 2018-02-04 18:02:05.765 [main] INFO com.zaxxer.hikari.HikariDataSource - exomiser-genome-hg19-1711 - Started. 2018-02-04 18:02:05.981 [main] INFO org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer - Opening MVStore from /public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db 2018-02-04 18:02:05.994 [main] WARN org.springframework.context.annotation.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:/public/home/pmc1/src/exomiser-cli-9.0.1/lib/exomiser-core-9.0.1.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$$EnhancerBySpringCGLIB$$4f85dbc6]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1] 2018-02-04 18:02:06.002 [main] INFO org.springframework.boot.autoconfigure.logging.AutoConfigurationReportLoggingInitializer -

Error starting ApplicationContext. To display the auto-configuration report re-run your application with 'debug' enabled. 2018-02-04 18:02:06.007 [main] ERROR org.springframework.boot.SpringApplication - Application startup 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:/public/home/pmc1/src/exomiser-cli-9.0.1/lib/exomiser-core-9.0.1.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$$EnhancerBySpringCGLIB$$4f85dbc6]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1] at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:588) at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:88) at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:366) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1264) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483) at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:693) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:360) at org.springframework.boot.SpringApplication.run(SpringApplication.java:303) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1118) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1107) 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:/public/home/pmc1/src/exomiser-cli-9.0.1/lib/exomiser-core-9.0.1.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$$EnhancerBySpringCGLIB$$4f85dbc6]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1] at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1193) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1095) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483) at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066) at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:585) ... 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$$EnhancerBySpringCGLIB$$4f85dbc6]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1] at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:467) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1173) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1067) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483) at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741) ... 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$$EnhancerBySpringCGLIB$$4f85dbc6]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1] at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:279) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1193) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1095) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483) at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:372) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1173) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1067) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483) at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208) at org.springframework.beans.factory.support.DefaultListableBeanFactory.addCandidateEntry(DefaultListableBeanFactory.java:1316) at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1282) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveMultipleBeans(DefaultListableBeanFactory.java:1160) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1096) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741) ... 45 common frames omitted Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$4f85dbc6]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1] at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:154) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:122) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:271) ... 70 common frames omitted Caused by: java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/src/exomiser-cli-9.0.1/data/1711_hg19/1711_hg19_variants.mv.db [1.4.195/1] at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:765) at org.h2.mvstore.FileStore.open(FileStore.java:179) at org.h2.mvstore.MVStore.(MVStore.java:347) at org.h2.mvstore.MVStore$Builder.open(MVStore.java:2930) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.openMvStore(GenomeAnalysisServiceConfigurer.java:212) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.(GenomeAnalysisServiceConfigurer.java:67) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration.(Hg19GenomeAnalysisServiceAutoConfiguration.java:44) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$4f85dbc6.() at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:142) ... 72 common frames omitted Caused by: java.io.IOException: Function not implemented at sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:90) at sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1115) at org.h2.store.fs.FileNio.tryLock(FilePathNio.java:121) at org.h2.mvstore.FileStore.open(FileStore.java:163) ... 83 common frames omitted

julesjacobsen commented 6 years ago

Never seen this issue - do you have permission set correctly?

hongenxu commented 6 years ago

thank you for your reply. What did you mean by permission set? Did you mean the files in data directory?

hongenxu commented 6 years ago

I upddated Exomiser to 10.0.0, and ran the test,

got the errors

Do you think it's about java versions or dependences ? My java version is

openjdk version "1.8.0_45" OpenJDK Runtime Environment (Zulu 8.7.0.5-linux64) (build 1.8.0_45-b14) OpenJDK 64-Bit Server VM (Zulu 8.7.0.5-linux64) (build 25.45-b02, mixed mode)

2018-03-14 13:03:12.393 [main] INFO  org.monarchinitiative.exomiser.cli.Main - Locale set to en_GB

 Welcome to:
  _____ _            _____                     _
 |_   _| |__   ___  | ____|_  _____  _ __ ___ (_)___  ___ _ __
   | | | '_ \ / _ \ |  _| \ \/ / _ \| '_ ` _ \| / __|/ _ \ '__|
   | | | | | |  __/ | |___ >  < (_) | | | | | | \__ \  __/ |
   |_| |_| |_|\___| |_____/_/\_\___/|_| |_| |_|_|___/\___|_|

 A Tool to Annotate and Prioritize Exome Variants     v10.0.0

2018-03-14 13:03:12.684 [main] INFO  org.monarchinitiative.exomiser.cli.Main - Starting Main on mu02 with PID 26279 (/public/home/pmc1/exomiser-cli-10.0.0/exomiser-cli-10.0.0.jar started by pmc1 in /public/home/pmc1/exomiser-cli-10.0.0)
2018-03-14 13:03:12.684 [main] INFO  org.monarchinitiative.exomiser.cli.Main - No active profile set, falling back to default profiles: default
2018-03-14 13:03:12.723 [main] INFO  org.springframework.context.annotation.AnnotationConfigApplicationContext - Refreshing org.springframework.context.annotation.AnnotationConfigApplicationContext@24ba9639: startup date [Wed Mar 14 13:03:12 CST 2018]; root of context hierarchy
2018-03-14 13:03:13.493 [main] INFO  org.monarchinitiative.exomiser.cli.config.MainConfig - Exomiser home: /public/home/pmc1/exomiser-cli-10.0.0
2018-03-14 13:03:13.504 [main] INFO  org.monarchinitiative.exomiser.cli.config.MainConfig - Exomiser data directory not defined in properties. Checking for default...
2018-03-14 13:03:13.504 [main] INFO  org.monarchinitiative.exomiser.cli.config.MainConfig - Found default data directory: /public/home/pmc1/exomiser-cli-10.0.0/data
2018-03-14 13:03:13.521 [main] INFO  com.zaxxer.hikari.HikariDataSource - exomiser-phenotype-1802 - Started.
2018-03-14 13:03:13.861 [main] WARN  org.springframework.context.annotation.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:/public/home/pmc1/exomiser-cli-10.0.0/lib/exomiser-core-10.0.0.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 'priorityFactoryImpl' defined in URL [jar:file:/public/home/pmc1/exomiser-cli-10.0.0/lib/exomiser-core-10.0.0.jar!/org/monarchinitiative/exomiser/core/prioritisers/PriorityFactoryImpl.class]: Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'randomWalkMatrix' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/phenotype/PrioritiserAutoConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.prioritisers.util.DataMatrix]: Factory method 'randomWalkMatrix' threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/exomiser-cli-10.0.0/data/1802_phenotype/rw_string_9_05.mv [1.4.195/1]
2018-03-14 13:03:13.862 [main] INFO  com.zaxxer.hikari.pool.HikariPool - exomiser-phenotype-1802 - Close initiated...
2018-03-14 13:03:13.898 [main] INFO  com.zaxxer.hikari.pool.HikariPool - exomiser-phenotype-1802 - Closed.
2018-03-14 13:03:13.907 [main] INFO  org.springframework.boot.autoconfigure.logging.AutoConfigurationReportLoggingInitializer -

Error starting ApplicationContext. To display the auto-configuration report re-run your application with 'debug' enabled.
2018-03-14 13:03:13.912 [main] ERROR org.springframework.boot.SpringApplication - Application startup 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:/public/home/pmc1/exomiser-cli-10.0.0/lib/exomiser-core-10.0.0.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 'priorityFactoryImpl' defined in URL [jar:file:/public/home/pmc1/exomiser-cli-10.0.0/lib/exomiser-core-10.0.0.jar!/org/monarchinitiative/exomiser/core/prioritisers/PriorityFactoryImpl.class]: Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'randomWalkMatrix' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/phenotype/PrioritiserAutoConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.prioritisers.util.DataMatrix]: Factory method 'randomWalkMatrix' threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/exomiser-cli-10.0.0/data/1802_phenotype/rw_string_9_05.mv [1.4.195/1]
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:588)
        at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:88)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:366)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1264)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
        at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:693)
        at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:360)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:303)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1118)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1107)
        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:/public/home/pmc1/exomiser-cli-10.0.0/lib/exomiser-core-10.0.0.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 'priorityFactoryImpl' defined in URL [jar:file:/public/home/pmc1/exomiser-cli-10.0.0/lib/exomiser-core-10.0.0.jar!/org/monarchinitiative/exomiser/core/prioritisers/PriorityFactoryImpl.class]: Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'randomWalkMatrix' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/phenotype/PrioritiserAutoConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.prioritisers.util.DataMatrix]: Factory method 'randomWalkMatrix' threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/exomiser-cli-10.0.0/data/1802_phenotype/rw_string_9_05.mv [1.4.195/1]
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1193)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1095)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:585)
        ... 18 common frames omitted
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'priorityFactoryImpl' defined in URL [jar:file:/public/home/pmc1/exomiser-cli-10.0.0/lib/exomiser-core-10.0.0.jar!/org/monarchinitiative/exomiser/core/prioritisers/PriorityFactoryImpl.class]: Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'randomWalkMatrix' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/phenotype/PrioritiserAutoConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.prioritisers.util.DataMatrix]: Factory method 'randomWalkMatrix' threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/exomiser-cli-10.0.0/data/1802_phenotype/rw_string_9_05.mv [1.4.195/1]
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1193)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1095)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835)
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741)
        ... 31 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'randomWalkMatrix' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/phenotype/PrioritiserAutoConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.prioritisers.util.DataMatrix]: Factory method 'randomWalkMatrix' threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/exomiser-cli-10.0.0/data/1802_phenotype/rw_string_9_05.mv [1.4.195/1]
        at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:599)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1173)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1067)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:835)
        at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:741)
        ... 45 common frames omitted
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.core.prioritisers.util.DataMatrix]: Factory method 'randomWalkMatrix' threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/exomiser-cli-10.0.0/data/1802_phenotype/rw_string_9_05.mv [1.4.195/1]
        at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:189)
        at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:588)
        ... 58 common frames omitted
Caused by: java.lang.IllegalStateException: Could not open file nio:/public/home/pmc1/exomiser-cli-10.0.0/data/1802_phenotype/rw_string_9_05.mv [1.4.195/1]
        at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:765)
        at org.h2.mvstore.FileStore.open(FileStore.java:179)
        at org.h2.mvstore.MVStore.<init>(MVStore.java:347)
        at org.h2.mvstore.MVStore$Builder.open(MVStore.java:2930)
        at org.monarchinitiative.exomiser.core.prioritisers.util.OffHeapDataMatrix.load(OffHeapDataMatrix.java:52)
        at org.monarchinitiative.exomiser.core.prioritisers.util.DataMatrixIO.loadOffHeapDataMatrix(DataMatrixIO.java:100)
        at org.monarchinitiative.exomiser.autoconfigure.phenotype.PrioritiserAutoConfiguration.randomWalkMatrix(PrioritiserAutoConfiguration.java:171)
        at org.monarchinitiative.exomiser.autoconfigure.phenotype.PrioritiserAutoConfiguration$$EnhancerBySpringCGLIB$$924fd706.CGLIB$randomWalkMatrix$1(<generated>)
        at org.monarchinitiative.exomiser.autoconfigure.phenotype.PrioritiserAutoConfiguration$$EnhancerBySpringCGLIB$$924fd706$$FastClassBySpringCGLIB$$11d07669.invoke(<generated>)
        at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:228)
        at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:358)
        at org.monarchinitiative.exomiser.autoconfigure.phenotype.PrioritiserAutoConfiguration$$EnhancerBySpringCGLIB$$924fd706.randomWalkMatrix(<generated>)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:162)
        ... 59 common frames omitted
Caused by: java.io.IOException: Function not implemented
        at sun.nio.ch.FileDispatcherImpl.lock0(Native Method)
        at sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:90)
        at sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1082)
        at org.h2.store.fs.FileNio.tryLock(FilePathNio.java:121)
        at org.h2.mvstore.FileStore.open(FileStore.java:163)
        ... 74 common frames omitted
julesjacobsen commented 6 years ago

This is very odd. It's not a JDK issue, at least not on Windows 10 x64 as I just tested version 10.0.0 on OpenJDK 9.0.4, OpenJDK (Zulu) 9.0.4 and Open JDK (Zulu) 8.0.163 as well as Oracle flavours.

Also we've run this on linux clusters running CentOS 7.3.1611 and OpenJDK 1.8.0_141 and various Ubuntu versions and MacOS whatever.

Might be something to do with your install - have a look at this link: http://lucene.472066.n3.nabble.com/java-io-IOException-Function-not-implemented-td684197.html

hongenxu commented 6 years ago

thanks for your reply. This error occures on HPCC clusters with CentOS. But Exomiser works on my own PC with centOS.

julesjacobsen commented 6 years ago

Did you read to the bottom of the link?

http://lucene.472066.n3.nabble.com/java-io-IOException-Function-not-implemented-tp684197p701263.html

The cluster might not have epoll enabled so that the lock file can be written. This isn't an Exomiser issue.