Error creating bean with name 'dataSource' when running test example on exomiser-cli-13.0.0

[evgonzal]

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:

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

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 :

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APPLICATION FAILED TO START

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Description:

Parameter 0 of method dataSource in org.springframework.boot.autoconfigure.jdbc.DataSourceConfiguration$Hikari required a single bean, but 3 were found:
- spring.datasource-org.springframework.boot.autoconfigure.jdbc.DataSourceProperties: defined in null
- phenotypeDataSourceProperties: defined by method 'phenotypeDataSourceProperties' in org.monarchinitiative.exomiser.autoconfigure.phenotype.PhenotypeProperties
- hg38genomeDataSourceProperties: defined by method 'hg38genomeDataSourceProperties' in org.monarchinitiative.exomiser.autoconfigure.genome.Hg38GenomeProperties

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

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How can I fix this problem?

Thanks in advance,

Eva

[julesjacobsen]

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]

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]

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]

Dear Jules,

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

Thanks!

Eva