CADD error

[shwetanavle]

I have downloaded the gnomad.genomes.r3.0.indel.tsv and gnomad.genomes.r3.0.indel.tsv.gz.tbi in my examiner folder and I gave the path in applications.properties as examiner-cli-12.1.0/data/2102_hg38/gnomad.genomes.r3.0.indel.tsv and both files are present in that data folder and I have made changes in iml file also but still I am getting the below error. Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiserCommandLineRunner': Unsatisfied dependency expressed through field 'analysisParser'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisParser' defined in URL [jar:file:/Users/admin/Desktop/exomiser-cli-12.1.0/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisParser.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Unsatisfied dependency expressed through method 'genomeAnalysisServiceProvider' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Bean instantiation via constructor failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$408163f2]: Constructor threw exception; nested exception is org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfigurationException: Failed to load/find file /Users/admin/Desktop/exomiser-cli-12.1.0/data/2102_hg38/exomiser-cli-12.1.0/data/2102_hg38/gnomad.genomes.r3.0.indel.tsv. Please check exomiser properties file points to a valid tabix .gz file. 2021-04-23 16:06:33.460 INFO 1628 --- [ main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled. 2021-04-23 16:06:33.463 ERROR 1628 --- [ main] o.s.boot.SpringApplication : Application run failed

org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'exomiserCommandLineRunner': Unsatisfied dependency expressed through field 'analysisParser'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisParser' defined in URL [jar:file:/Users/admin/Desktop/exomiser-cli-12.1.0/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisParser.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Unsatisfied dependency expressed through method 'genomeAnalysisServiceProvider' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Bean instantiation via constructor failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$408163f2]: Constructor threw exception; nested exception is org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfigurationException: Failed to load/find file /Users/admin/Desktop/exomiser-cli-12.1.0/data/2102_hg38/exomiser-cli-12.1.0/data/2102_hg38/gnomad.genomes.r3.0.indel.tsv. Please check exomiser properties file points to a valid tabix .gz file. at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:596) at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:90) at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessProperties(AutowiredAnnotationBeanPostProcessor.java:374) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1395) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:592) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:849) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:877) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:549) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:775) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397) at org.springframework.boot.SpringApplication.run(SpringApplication.java:316) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1260) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1248) at org.monarchinitiative.exomiser.cli.Main.main(Main.java:44) Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'analysisParser' defined in URL [jar:file:/Users/admin/Desktop/exomiser-cli-12.1.0/lib/exomiser-core-12.1.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisParser.class]: Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Unsatisfied dependency expressed through method 'genomeAnalysisServiceProvider' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Bean instantiation via constructor failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$408163f2]: Constructor threw exception; nested exception is org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfigurationException: Failed to load/find file /Users/admin/Desktop/exomiser-cli-12.1.0/data/2102_hg38/exomiser-cli-12.1.0/data/2102_hg38/gnomad.genomes.r3.0.indel.tsv. Please check exomiser properties file points to a valid tabix .gz file. at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:769) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:218) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1325) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1171) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:277) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1247) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1167) at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:593) ... 18 common frames omitted Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'genomeAnalysisServiceProvider' defined in class path resource [org/monarchinitiative/exomiser/autoconfigure/genome/GenomeAnalysisServiceAutoConfiguration.class]: Unsatisfied dependency expressed through method 'genomeAnalysisServiceProvider' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Bean instantiation via constructor failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$408163f2]: Constructor threw exception; nested exception is org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfigurationException: Failed to load/find file /Users/admin/Desktop/exomiser-cli-12.1.0/data/2102_hg38/exomiser-cli-12.1.0/data/2102_hg38/gnomad.genomes.r3.0.indel.tsv. Please check exomiser properties file points to a valid tabix .gz file. at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:769) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:509) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1305) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1144) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:277) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1247) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1167) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:857) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:760) ... 31 common frames omitted Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration': Bean instantiation via constructor failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$408163f2]: Constructor threw exception; nested exception is org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfigurationException: Failed to load/find file /Users/admin/Desktop/exomiser-cli-12.1.0/data/2102_hg38/exomiser-cli-12.1.0/data/2102_hg38/gnomad.genomes.r3.0.indel.tsv. Please check exomiser properties file points to a valid tabix .gz file. at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:304) at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1325) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1171) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:392) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1305) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1144) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:277) at org.springframework.beans.factory.support.DefaultListableBeanFactory.addCandidateEntry(DefaultListableBeanFactory.java:1463) at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1427) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveMultipleBeans(DefaultListableBeanFactory.java:1295) at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1205) at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1167) at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:857) at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:760) ... 45 common frames omitted Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$408163f2]: Constructor threw exception; nested exception is org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfigurationException: Failed to load/find file /Users/admin/Desktop/exomiser-cli-12.1.0/data/2102_hg38/exomiser-cli-12.1.0/data/2102_hg38/gnomad.genomes.r3.0.indel.tsv. Please check exomiser properties file points to a valid tabix .gz file. at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:184) at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:117) at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:300) ... 71 common frames omitted Caused by: org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfigurationException: Failed to load/find file /Users/admin/Desktop/exomiser-cli-12.1.0/data/2102_hg38/exomiser-cli-12.1.0/data/2102_hg38/gnomad.genomes.r3.0.indel.tsv. Please check exomiser properties file points to a valid tabix .gz file. at org.monarchinitiative.exomiser.autoconfigure.genome.TabixDataSourceLoader.load(TabixDataSourceLoader.java:50) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeDataSourceLoader.getTabixDataSourceOrDefault(GenomeDataSourceLoader.java:134) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeDataSourceLoader.(GenomeDataSourceLoader.java:86) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeDataSourceLoader.load(GenomeDataSourceLoader.java:68) at org.monarchinitiative.exomiser.autoconfigure.genome.GenomeAnalysisServiceConfigurer.(GenomeAnalysisServiceConfigurer.java:69) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration.(Hg38GenomeAnalysisServiceAutoConfiguration.java:46) at org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeAnalysisServiceAutoConfiguration$$EnhancerBySpringCGLIB$$408163f2.() at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:64) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:481) at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:172) ... 73 common frames omitted Caused by: java.io.FileNotFoundException: /Users/admin/Desktop/exomiser-cli-12.1.0/data/2102_hg38/exomiser-cli-12.1.0/data/2102_hg38/gnomad.genomes.r3.0.indel.tsv (No such file or directory) at java.base/java.io.RandomAccessFile.open0(Native Method) at java.base/java.io.RandomAccessFile.open(RandomAccessFile.java:347) at java.base/java.io.RandomAccessFile.(RandomAccessFile.java:261) at java.base/java.io.RandomAccessFile.(RandomAccessFile.java:216) at htsjdk.samtools.seekablestream.SeekableFileStream.(SeekableFileStream.java:47) at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:103) at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:77) at htsjdk.tribble.readers.TabixReader.(TabixReader.java:109) at org.monarchinitiative.exomiser.autoconfigure.genome.TabixDataSourceLoader.load(TabixDataSourceLoader.java:48) ... 85 common frames omitted

Help would be appreciated Thank you in advance

[stereotypy]

I was having some issues getting started with paths too, you can see from the output

Failed to load/find file /Users/admin/Desktop/exomiser-cli-12.1.0/data/2102_hg38/exomiser-cli-12.1.0/data/2102_hg38/gnomad.genomes.r3.0.indel.tsv.

Your path is being doubled up, keep tweaking the paths/root dirs in the file to fix it, lots of trial and error, that's what I did.