Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled.

[FAFUshiyan]

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

Run the command as follows：

java -Xms2g -Xmx4g -jar /genetics/home/shiyan/software/exomiser-cli-13.0.1/exomiser-cli-13.0.1.jar --analysis /genetics/home/shiyan/software/exomiser-cli-13.0.1/examples/test-analysis-exome.yml --spring.config.location=/genetics/home/shiyan/software/exomiser-cli-13.0.1/application.properties --output Xp

2022-05-22 19:14:54.616 WARN 52052 --- [ 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:/genetics/home/shiyan/software/exomiser-cli-13.0.1/exomiser-cli-13.0.1.jar!/org/monarchinitiative/exomiser/cli/ExomiserCommandLineRunner.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiser' defined in URL [jar:file:/genetics/home/shiyan/software/exomiser-cli-13.0.1/lib/exomiser-core-13.0.1.jar!/org/monarchinitiative/exomiser/core/Exomiser.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisFactory' defined in URL [jar:file:/genetics/home/shiyan/software/exomiser-cli-13.0.1/lib/exomiser-core-13.0.1.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisFactory.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Unsatisfied dependency expressed through method 'genomeAnalysisServiceProvider' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration': Bean instantiation via constructor failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$bd150392]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/cluster/huawei-genetics/project/shiyan/Exomiser_data/2109_hg19/2109_hg19_variants.mv.db [1.4.200/1] 2022-05-22 19:14:54.629 INFO 52052 --- [ main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled. 2022-05-22 19:14:54.644 ERROR 52052 --- [ main] o.s.boot.SpringApplication : Application run failed

org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiserCommandLineRunner' defined in URL [jar:file:/genetics/home/shiyan/software/exomiser-cli-13.0.1/exomiser-cli-13.0.1.jar!/org/monarchinitiative/exomiser/cli/ExomiserCommandLineRunner.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiser' defined in URL [jar:file:/genetics/home/shiyan/software/exomiser-cli-13.0.1/lib/exomiser-core-13.0.1.jar!/org/monarchinitiative/exomiser/core/Exomiser.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisFactory' defined in URL [jar:file:/genetics/home/shiyan/software/exomiser-cli-13.0.1/lib/exomiser-core-13.0.1.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisFactory.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Unsatisfied dependency expressed through method 'genomeAnalysisServiceProvider' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration': Bean instantiation via constructor failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg19GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$bd150392]: Constructor threw exception; nested exception is java.lang.IllegalStateException: Could not open file nio:/cluster/huawei-genetics/project/shiyan/Exomiser_data/2109_hg19/2109_hg19_variants.mv.db [1.4.200/1]

[julesjacobsen]

are you able to access the file /cluster/huawei-genetics/project/shiyan/Exomiser_data/2109_hg19/2109_hg19_variants.mv.db as suggested by the error message?

[FAFUshiyan]

Yes, I have access to.

[julesjacobsen]

Could it be a permissions issue with the user running the application? I'm not sure what the problem might be, assuming all the data is in the correct place as specified in the application.properties and that the files are not corrupted (there is a sha256 file to check against)

[julesjacobsen]

Closing due to lack of response.