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Application run failed #586

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abrusell opened this issue Jan 9, 2025 · 2 comments
Open

Application run failed #586

abrusell opened this issue Jan 9, 2025 · 2 comments

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@abrusell
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abrusell commented Jan 9, 2025

Hi,
exomiser 14.1.0 run with 2410 data release keeps failing and I'm not sure for what reason...
I don't understand why it keeps deserialising hg19 files although hg38 genome assembly is specified both in application.properties and in yml input files

Here is the error log:
`
Welcome to:

|_ | |_ ___ | | _____ _ __ ___ ()_ ___ _ __
| | | '_ \ / _ \ | | \ / / _ | ' ` _ | / |/ _ \ '|
| | | | | | / | |_ > < () | | | | | | _ \ / |
|| || |_|_| |/_/__/|| || |||/___|_|

A Tool to Annotate and Prioritize Exome Variants v14.1.0

2025-01-09T14:56:07.036+01:00 INFO 26562 --- [ main] o.monarchinitiative.exomiser.cli.Main : Starting Main using Java 21.0.5 with PID 26562 (/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/exomiser-cli-14.1.0.jar started by abrusell in /g100_work/OPBG2_prod2023/WGS/Results/Cordeddu/fam31/tmp)
2025-01-09T14:56:07.044+01:00 INFO 26562 --- [ main] o.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to 1 default profile: "default"
2025-01-09T14:56:08.307+01:00 INFO 26562 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0
2025-01-09T14:56:08.320+01:00 INFO 26562 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/data
2025-01-09T14:56:08.326+01:00 INFO 26562 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/data/2410_hg19/2410_hg19_transcripts_ensembl.ser
2025-01-09T14:56:15.635+01:00 INFO 26562 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 7.308 sec.
2025-01-09T14:56:18.358+01:00 INFO 26562 --- [ main] o.m.e.c.g.dao.ClinVarWhiteListReader : Reading ClinVar whitelist...
2025-01-09T14:56:18.392+01:00 INFO 26562 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'clinvar' opened with 3021594 entries
2025-01-09T14:56:23.069+01:00 INFO 26562 --- [ main] o.m.e.c.g.dao.ClinVarWhiteListReader : Read 246517 ClinVar whitelist variants in 4710 ms
2025-01-09T14:56:23.122+01:00 INFO 26562 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Loaded 246517 whitelist variants
2025-01-09T14:56:23.330+01:00 INFO 26562 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'alleles' opened with 891879779 entries
2025-01-09T14:56:23.403+01:00 INFO 26562 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'clinvar' opened with 3021594 entries
2025-01-09T14:56:27.033+01:00 INFO 26562 --- [ main] o.m.e.core.genome.dao.ClinVarDaoMvStore : Created 19083 ClinVar gene stats in 3630 ms
2025-01-09T14:56:27.083+01:00 INFO 26562 --- [ main] com.zaxxer.hikari.HikariDataSource : 2410_hg19_genome - Starting...
2025-01-09T14:56:27.583+01:00 INFO 26562 --- [ main] com.zaxxer.hikari.pool.HikariPool : 2410_hg19_genome - Added connection conn0: url=jdbc:h2:file:/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/data/2410_hg19/2410_hg19_genome user=SA
2025-01-09T14:56:27.586+01:00 INFO 26562 --- [ main] com.zaxxer.hikari.HikariDataSource : 2410_hg19_genome - Start completed.
2025-01-09T14:56:28.533+01:00 INFO 26562 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/data/2410_hg38/2410_hg38_transcripts_refseq.ser
2025-01-09T14:56:49.325+01:00 INFO 26562 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 20.79 sec.
2025-01-09T14:56:55.279+01:00 WARN 26562 --- [ main] s.c.a.AnnotationConfigApplicationContext : Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiserCommandLineRunner' defined in URL [jar:file:/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/exomiser-cli-14.1.0.jar!/org/monarchinitiative/exomiser/cli/ExomiserCommandLineRunner.class]: Unsatisfied dependency expressed through constructor parameter 0: Error creating bean with name 'exomiser' defined in URL [jar:file:/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/lib/exomiser-core-14.1.0.jar!/org/monarchinitiative/exomiser/core/Exomiser.class]: Unsatisfied dependency expressed through constructor parameter 0: Error creating bean with name 'analysisFactory' defined in URL [jar:file:/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/lib/exomiser-core-14.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisFactory.class]: Unsatisfied dependency expressed through constructor parameter 0: 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: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$SpringCGLIB$$0]: Constructor threw exception
2025-01-09T14:56:55.293+01:00 INFO 26562 --- [ main] com.zaxxer.hikari.HikariDataSource : 2410_hg19_genome - Shutdown initiated...
2025-01-09T14:56:55.297+01:00 INFO 26562 --- [ main] com.zaxxer.hikari.HikariDataSource : 2410_hg19_genome - Shutdown completed.
2025-01-09T14:56:55.318+01:00 INFO 26562 --- [ main] .s.b.a.l.ConditionEvaluationReportLogger :

Error starting ApplicationContext. To display the condition evaluation report re-run your application with 'debug' enabled.
2025-01-09T14:56:55.354+01:00 ERROR 26562 --- [ main] o.s.boot.SpringApplication : Application run failed

org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiserCommandLineRunner' defined in URL [jar:file:/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/exomiser-cli-14.1.0.jar!/org/monarchinitiative/exomiser/cli/ExomiserCommandLineRunner.class]: Unsatisfied dependency expressed through constructor parameter 0: Error creating bean with name 'exomiser' defined in URL [jar:file:/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/lib/exomiser-core-14.1.0.jar!/org/monarchinitiative/exomiser/core/Exomiser.class]: Unsatisfied dependency expressed through constructor parameter 0: Error creating bean with name 'analysisFactory' defined in URL [jar:file:/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/lib/exomiser-core-14.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisFactory.class]: Unsatisfied dependency expressed through constructor parameter 0: 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: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$SpringCGLIB$$0]: Constructor threw exception
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:798) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:237) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1355) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1192) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:325) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:323) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:975) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:959) ~[spring-context-6.1.4.jar:6.1.4]
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:624) ~[spring-context-6.1.4.jar:6.1.4]
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:754) ~[spring-boot-3.2.3.jar:3.2.3]
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:456) ~[spring-boot-3.2.3.jar:3.2.3]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:334) ~[spring-boot-3.2.3.jar:3.2.3]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1354) ~[spring-boot-3.2.3.jar:3.2.3]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343) ~[spring-boot-3.2.3.jar:3.2.3]
at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53) ~[exomiser-cli-14.1.0.jar:na]
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiser' defined in URL [jar:file:/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/lib/exomiser-core-14.1.0.jar!/org/monarchinitiative/exomiser/core/Exomiser.class]: Unsatisfied dependency expressed through constructor parameter 0: Error creating bean with name 'analysisFactory' defined in URL [jar:file:/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/lib/exomiser-core-14.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisFactory.class]: Unsatisfied dependency expressed through constructor parameter 0: 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: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$SpringCGLIB$$0]: Constructor threw exception
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:798) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:237) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1355) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1192) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:325) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:323) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1443) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1353) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:907) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:785) ~[spring-beans-6.1.4.jar:6.1.4]
... 18 common frames omitted
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisFactory' defined in URL [jar:file:/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/lib/exomiser-core-14.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisFactory.class]: Unsatisfied dependency expressed through constructor parameter 0: 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: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$SpringCGLIB$$0]: Constructor threw exception
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:798) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:237) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1355) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1192) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:325) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:323) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1443) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1353) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:907) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:785) ~[spring-beans-6.1.4.jar:6.1.4]
... 32 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: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$SpringCGLIB$$0]: Constructor threw exception
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:798) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:542) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1335) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1165) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:325) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:323) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1443) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1353) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:907) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:785) ~[spring-beans-6.1.4.jar:6.1.4]
... 46 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$SpringCGLIB$$0]: Constructor threw exception
at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:318) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:306) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1355) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1192) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:325) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:323) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:409) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1335) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1165) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:325) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:323) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.addCandidateEntry(DefaultListableBeanFactory.java:1689) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1653) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveMultipleBeans(DefaultListableBeanFactory.java:1492) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1392) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1353) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:907) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:785) ~[spring-beans-6.1.4.jar:6.1.4]
... 60 common frames omitted
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$SpringCGLIB$$0]: Constructor threw exception
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:223) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:111) ~[spring-beans-6.1.4.jar:6.1.4]
at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:315) ~[spring-beans-6.1.4.jar:6.1.4]
... 86 common frames omitted
Caused by: org.h2.mvstore.MVStoreException: Could not open file /g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/data/2410_hg38/2410_hg38_clinvar.mv.db [2.2.224/1]
at org.h2.mvstore.DataUtils.newMVStoreException(DataUtils.java:996) ~[h2-2.2.224.jar:2.2.224]
at org.h2.mvstore.SingleFileStore.open(SingleFileStore.java:126) ~[h2-2.2.224.jar:2.2.224]
at org.h2.mvstore.SingleFileStore.open(SingleFileStore.java:81) ~[h2-2.2.224.jar:2.2.224]
at org.h2.mvstore.MVStore.(MVStore.java:286) ~[h2-2.2.224.jar:2.2.224]
at org.h2.mvstore.MVStore$Builder.open(MVStore.java:2035) ~[h2-2.2.224.jar:2.2.224]
at org.monarchinitiative.exomiser.autoconfigure.genome.MvStoreDataSourceLoader.openMvStore(MvStoreDataSourceLoader.java:39) ~[exomiser-spring-boot-autoconfigure-14.1.0.jar:na]
at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeDataSourceLoader.loadClinVarMvStore(GenomeDataSourceLoader.java:112) ~[exomiser-spring-boot-autoconfigure-14.1.0.jar:na]
at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeDataSourceLoader.(GenomeDataSourceLoader.java:74) ~[exomiser-spring-boot-autoconfigure-14.1.0.jar:na]
at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.(GenomeAnalysisServiceConfigurer.java:61) ~[exomiser-spring-boot-autoconfigure-14.1.0.jar:na]
at org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration.(Hg38GenomeAnalysisServiceAutoConfiguration.java:53) ~[exomiser-spring-boot-autoconfigure-14.1.0.jar:na]
at org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$SpringCGLIB$$0.() ~[exomiser-spring-boot-autoconfigure-14.1.0.jar:na]
at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(Unknown Source) ~[na:na]
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Unknown Source) ~[na:na]
at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source) ~[na:na]
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:210) ~[spring-beans-6.1.4.jar:6.1.4]
... 88 common frames omitted
Caused by: java.nio.file.NoSuchFileException: /g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/data/2410_hg38/2410_hg38_clinvar.mv.db
at java.base/sun.nio.fs.UnixException.translateToIOException(Unknown Source) ~[na:na]
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source) ~[na:na]
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source) ~[na:na]
at java.base/sun.nio.fs.UnixFileSystemProvider.newFileChannel(Unknown Source) ~[na:na]
at java.base/java.nio.channels.FileChannel.open(Unknown Source) ~[na:na]
at org.h2.store.fs.disk.FilePathDisk.open(FilePathDisk.java:468) ~[h2-2.2.224.jar:2.2.224]
at org.h2.mvstore.SingleFileStore.open(SingleFileStore.java:112) ~[h2-2.2.224.jar:2.2.224]
... 101 common frames omitted
`

I've attached the application.properties and the yml input files

Thanks
@abrusell
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abrusell commented Jan 9, 2025

application.properties.zip
ANDE81_prob_genomiser.yml.zip

@julesjacobsen
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julesjacobsen commented Jan 10, 2025 •
edited
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Your application.properties (trimming out the commented lines) looks like this:

exomiser.data-directory=/g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/data

## optional data sources ##
remm.version=0.4
cadd.version=1.6

### hg19 assembly ###
exomiser.hg19.data-version=2410

### hg38 assembly ###
# To enable analysis of samples called against the hg38 assembly copy the hg19 above and just replace the hg19 with hg38
exomiser.hg38.data-version=2410
exomiser.hg38.transcript-source=refseq
exomiser.hg38.cadd-snv-path=/g100_work/OPBG2_prod2023/NGS_tools/CADD_v1.6/data/prescored/GRCh38_v1.6/no_anno/whole_genome_SNVs.tsv.gz
exomiser.hg38.cadd-in-del-path=/g100_work/OPBG2_prod2023/NGS_tools/CADD_v1.6/data/prescored/GRCh38_v1.6/no_anno/gnomad.genomes.r3.0.indel.tsv.gz
exomiser.hg38.remm-path=/g100_work/OPBG2_prod2023/db/hg38/REMM/ReMM.v${remm.version}.hg38.tsv.gz

### phenotypes ###
exomiser.phenotype.data-version=2410

To stop Exomiser loading the hg19 data, you need to comment out/ remove the exomiser.hg19.data-version=2410 line.

The last error thrown in the message you pasted states:

Caused by: java.nio.file.NoSuchFileException: /g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/data/2410_hg38/2410_hg38_clinvar.mv.db

Did you extract all the files from the 2410_hg38.zip download and run the checksum? e.g. running sha256sum -c 2410_hg38.sha256 from the /g100_work/OPBG2_prod2023/NGS_tools/exomiser-cli-14.1.0/ directory.

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