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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Error creating bean with name 'dataSource' when running test example on exomiser-cli-13.0.0 #412

Closed evgonzal closed 2 years ago

evgonzal commented 2 years ago

Good morning

I am getting the current error when running the example test after installing exomiser-cli-13.0.0 on a mac laptop:

I run: java -Xms4g -Xmx8g -jar exomiser-cli-13.0.0.jar --analysis examples/test-analysis-exome.yml

I get: Welcome to:

| | | _ | __| ____ _ ()__ _ | | | ' \ / \ | | \ \/ / | ' ` | / |/ _ \ '| | | | | | | / | | > < () | | | | | | __ \ _/ | || || ||_| |__//__/|| || |||/\|_|

A Tool to Annotate and Prioritize Exome Variants v13.0.0

2021-11-13 13:09:04.630 INFO 25107 --- [ main] org.monarchinitiative.exomiser.cli.Main : Starting Main using Java 11.0.9.1 on MacBook-Pro.local with PID 25107 (/Users/Eva/BIOINFO/exomiser-cli-13.0.0/exomiser-cli-13.0.0.jar started by Eva in /Users/Eva/BIOINFO/exomiser-cli-13.0.0) 2021-11-13 13:09:04.634 INFO 25107 --- [ main] org.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to default profiles: default 2021-11-13 13:09:05.490 INFO 25107 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /Users/Eva/BIOINFO/exomiser-cli-13.0.0 2021-11-13 13:09:05.500 INFO 25107 --- [ main] o.m.exomiser.cli.config.MainConfig : Data source directory defined in properties as: ./data 2021-11-13 13:09:05.501 INFO 25107 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /Users/Eva/BIOINFO/exomiser-cli-13.0.0/./data 2021-11-13 13:09:05.505 INFO 25107 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /Users/Eva/BIOINFO/exomiser-cli-13.0.0/./data/2109_hg38/2109_hg38_transcripts_refseq.ser 2021-11-13 13:09:08.446 INFO 25107 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 2.94 sec. 2021-11-13 13:09:09.350 INFO 25107 --- [ main] o.m.e.c.g.dao.VariantWhiteListLoader : Loading variant whitelist from: /Users/Eva/BIOINFO/exomiser-cli-13.0.0/./data/2109_hg38/2109_hg38_clinvar_whitelist.tsv.gz 2021-11-13 13:09:09.556 INFO 25107 --- [ main] o.m.e.c.g.dao.VariantWhiteListLoader : Loaded 112277 variants into whitelist 2021-11-13 13:09:10.103 INFO 25107 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg38 genome analysis service 2021-11-13 13:09:11.399 INFO 25107 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: /Users/Eva/BIOINFO/exomiser-cli-13.0.0/results 2021-11-13 13:09:11.443 WARN 25107 --- [ main] s.c.a.AnnotationConfigApplicationContext : Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'dataSource' defined in class path resource [org/springframework/boot/autoconfigure/jdbc/DataSourceConfiguration$Hikari.class]: Unsatisfied dependency expressed through method 'dataSource' parameter 0; nested exception is org.springframework.beans.factory.NoUniqueBeanDefinitionException: No qualifying bean of type 'org.springframework.boot.autoconfigure.jdbc.DataSourceProperties' available: expected single matching bean but found 3: spring.datasource-org.springframework.boot.autoconfigure.jdbc.DataSourceProperties,phenotypeDataSourceProperties,hg38genomeDataSourceProperties 2021-11-13 13:09:11.490 INFO 25107 --- [ main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled. 2021-11-13 13:09:11.508 ERROR 25107 --- [ main] o.s.b.d.LoggingFailureAnalysisReporter :

APPLICATION FAILED TO START

Description:

Parameter 0 of method dataSource in org.springframework.boot.autoconfigure.jdbc.DataSourceConfiguration$Hikari required a single bean, but 3 were found:

Action:

Consider marking one of the beans as @Primary, updating the consumer to accept multiple beans, or using @Qualifier to identify the bean that should be consumed

How can I fix this problem?

Thanks in advance,

Eva

julesjacobsen commented 2 years ago

Hi Eva,

Are you trying to only load the hg38 and phenotype data? I've published release 13.0.1 with a fix for this now.

evgonzal commented 2 years ago

Dear Jules,

Thanks for your response. We have downloaded the new fixed version 13.0.1 but it seems that now I can get other errors. I am able at least to start running exomiser but now it throws an error in this step: ConditionEvaluationReportLoggingListener.

I paste the error I get.

Thanks in advance for your help

Eva

java -Xms2g -Xmx4g -jar /Users/Eva/BIOINFO/exomiser-cli-13.0.1/exomiser-cli-13.0.1.jar --analysis /Users/Eva/BIOINFO/exomiser-cli-13.0.1/examples/test-analysis-exome.yml --spring.config.location=/Users/Eva/BIOINFO/exomiser-cli-13.0.1/application.properties

Welcome to:

| | | _ | __| ____ _ ()__ _ | | | ' \ / \ | | \ \/ / | ' ` | / |/ _ \ '| | | | | | | / | | > < () | | | | | | __ \ _/ | || || ||_| |__//__/|| || |||/\|_|

A Tool to Annotate and Prioritize Exome Variants v13.0.1

2021-11-24 19:18:51.234 INFO 36926 --- [ main] org.monarchinitiative.exomiser.cli.Main : Starting Main using Java 11.0.9.1 on MacBook-Pro.local with PID 36926 (/Users/Eva/BIOINFO/exomiser-cli-13.0.1/exomiser-cli-13.0.1.jar started by Eva in /Users/Eva/BIOINFO) 2021-11-24 19:18:51.237 INFO 36926 --- [ main] org.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to default profiles: default 2021-11-24 19:18:52.034 INFO 36926 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /Users/Eva/BIOINFO/exomiser-cli-13.0.1 2021-11-24 19:18:52.043 INFO 36926 --- [ main] o.m.exomiser.cli.config.MainConfig : Data source directory defined in properties as: /Users/Eva/BIOINFO/exomiser-cli-13.0.1/data 2021-11-24 19:18:52.043 INFO 36926 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /Users/Eva/BIOINFO/exomiser-cli-13.0.1/data 2021-11-24 19:18:52.048 INFO 36926 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /Users/Eva/BIOINFO/exomiser-cli-13.0.1/data/2109_hg38/2109_hg38_transcripts_refseq.ser 2021-11-24 19:18:55.105 INFO 36926 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 3.056 sec. 2021-11-24 19:18:56.585 INFO 36926 --- [ main] o.m.e.c.g.dao.VariantWhiteListLoader : Loading variant whitelist from: /Users/Eva/BIOINFO/exomiser-cli-13.0.1/data/2109_hg38/2109_hg38_clinvar_whitelist.tsv.gz 2021-11-24 19:18:56.896 INFO 36926 --- [ main] o.m.e.c.g.dao.VariantWhiteListLoader : Loaded 112277 variants into whitelist 2021-11-24 19:18:57.527 INFO 36926 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg38 genome analysis service 2021-11-24 19:19:03.222 INFO 36926 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: /Users/Eva/BIOINFO/exomiser-cli-13.0.1/results 2021-11-24 19:19:03.417 INFO 36926 --- [ main] org.monarchinitiative.exomiser.cli.Main : Started Main in 12.799 seconds (JVM running for 13.191) 2021-11-24 19:19:03.768 INFO 36926 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Exomiser running... 2021-11-24 19:19:03.777 INFO 36926 --- [ main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled. 2021-11-24 19:19:03.796 ERROR 36926 --- [ main] o.s.boot.SpringApplication : Application run failed

java.lang.IllegalStateException: Failed to execute CommandLineRunner at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:794) at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:775) at org.springframework.boot.SpringApplication.run(SpringApplication.java:345) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332) at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53) Caused by: org.monarchinitiative.exomiser.core.genome.UnsupportedGenomeAssemblyException: Assembly hg19 not supported in this instance. Supported assemblies are: [hg38] at org.monarchinitiative.exomiser.core.analysis.JobParser.checkAssemblySupportedOrThrowException(JobParser.java:135) at org.monarchinitiative.exomiser.core.analysis.JobParser.parseSample(JobParser.java:86) at org.monarchinitiative.exomiser.core.analysis.AnalysisParser.parseSample(AnalysisParser.java:99) at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:67) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJob(ExomiserCommandLineRunner.java:79) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJobs(ExomiserCommandLineRunner.java:62) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.run(ExomiserCommandLineRunner.java:57) at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:791) ... 5 common frames omitted

julesjacobsen commented 2 years ago

You're trying to analyse an hg19 sample on an Exomiser instance which only has hg38 data loaded.

See the error:

Caused by: org.monarchinitiative.exomiser.core.genome.UnsupportedGenomeAssemblyException: Assembly hg19 not supported in this instance. Supported assemblies are: [hg38]

Check that the assembly is correct in the sample, or make sure you enable hg19 in the application.properties file. There is an example of this in the distribution.

evgonzal commented 2 years ago

Dear Jules,

You're right. I finally managed to run exomiser v13.0.1.

Thanks!

Eva