Problem running Exomiser-cli after installation on CentOS 7.

[gilskim]

I've executed as the below command. java -Xms2g -Xmx4g -jar exomiser-cli-11.0.0.jar --help

When executing this command, I got the error message.

17:23:40.472 [main] INFO org.monarchinitiative.exomiser.cli.Main - Locale set to en_GB

Welcome to:

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A Tool to Annotate and Prioritize Exome Variants v11.0.0

2019-05-14 17:23:41.086 INFO 21506 --- [ main] org.monarchinitiative.exomiser.cli.Main : Starting Main on Server20 with PID 21506 (/Tools/toolsForbanchmark/exomiser_v11/exomiser-cli-11.0.0/exomiser-cli-11.0.0.jar started by root in /Tools/toolsForbanchmark/exomiser_v11/exomiser-cli-11.0.0) 2019-05-14 17:23:41.088 INFO 21506 --- [ main] org.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to default profiles: default 2019-05-14 17:23:41.134 INFO 21506 --- [ main] s.c.a.AnnotationConfigApplicationContext : Refreshing org.springframework.context.annotation.AnnotationConfigApplicationContext@149e0f5d: startup date [Tue May 14 17:23:41 KST 2019]; root of context hierarchy 2019-05-14 17:23:42.043 INFO 21506 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /Tools/toolsForbanchmark/exomiser_v11/exomiser-cli-11.0.0 2019-05-14 17:23:42.058 INFO 21506 --- [ main] o.m.exomiser.cli.config.MainConfig : Data source directory defined in properties as: data 2019-05-14 17:23:42.058 INFO 21506 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /Tools/toolsForbanchmark/exomiser_v11/exomiser-cli-11.0.0/data 2019-05-14 17:23:42.077 INFO 21506 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Starting... 2019-05-14 17:23:42.386 INFO 21506 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Start completed. 2019-05-14 17:23:43.805 INFO 21506 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-genome-hg19-1811 - Starting... 2019-05-14 17:23:43.816 INFO 21506 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-genome-hg19-1811 - Start completed. 2019-05-14 17:23:43.819 INFO 21506 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /Tools/toolsForbanchmark/exomiser_v11/exomiser-cli-11.0.0/data/1811_hg19/1811_hg19_transcripts_ensembl.ser 2019-05-14 17:23:48.851 INFO 21506 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 5.03 sec. 2019-05-14 17:23:49.660 INFO 21506 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Opening LOCAL data from source: /Tools/toolsForbanchmark/exomiser_v11/exomiser-cli-11.0.0/data/1811_hg19/data/1811_hg19/local_frequency_test.tsv.gz 2019-05-14 17:23:49.675 WARN 21506 --- [ main] s.c.a.AnnotationConfigApplicationContext : 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:/Tools/toolsForbanchmark/exomiser_v11/exomiser-cli-11.0.0/lib/exomiser-core-11.0.0.jar!/org/monarchinitiative/exomiser/core/analysis/AnalysisParser.class]: Unsatisfied dependency expressed through constructor parameter 1; 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$$EnhancerBySpringCGLIB$$f5204ec]: Constructor threw exception; nested exception is org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfigurationException: Failed to load/find file /Tools/toolsForbanchmark/exomiser_v11/exomiser-cli-11.0.0/data/1811_hg19/data/1811_hg19/local_frequency_test.tsv.gz. Please check exomiser properties file points to a valid tabix .gz file. 2019-05-14 17:23:49.676 INFO 21506 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Shutdown initiated... 2019-05-14 17:23:49.681 INFO 21506 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Shutdown completed.

[julesjacobsen]

Hi @gilskim the clue to the error is in the error message:

 org.monarchinitiative.exomiser.autoconfigure.ExomiserAutoConfigurationException: Failed to load/find file /Tools/toolsForbanchmark/exomiser_v11/exomiser-cli-11.0.0/data/1811_hg19/data/1811_hg19/local_frequency_test.tsv.gz. Please check exomiser properties file points to a valid tabix .gz file

Does that file exist? Is it a proper tabix file? Do you or the application have permissions to read it?

[gilskim]

Hi, @julesjacobsen

Thank you for your help.

I can't find local_frequency_test.tsv.gz in /Tools/toolsForbanchmark/exomiser_v11/exomiser-cli-11.0.0/data/1811_hg19/data/1811_hg19/.

I just refer to this site (https://github.com/exomiser/Exomiser/tree/master/exomiser-cli) to complete the configuration after installation of exomiser.

So, I thought that I did all of the work to use the exomiser.

Could you tell me about the website with instructions to solve this problem. (I can't find the suitable website....)

[julesjacobsen]

The application.properties file states this is optional data. If you have local frequencies, then enable it and point the path to their location. If not, leave the configuration as it is - it is set-up for default behaviour and will function correctly.

[gilskim]

I do not have any local frequencies.

I have downloaded data using below command. wget https://data.monarchinitiative.org/exomiser/latest/1811_hg19.zip

the list of files in 1811_hg19 directory. 1811_hg19_genome.h2.db 1811_hg19_transcripts_refseq.ser 1811_hg19_variants.mv.db 1811_hg19_transcripts_ensembl.ser 1811_hg19_transcripts_ucsc.ser

Also, I did nothing about setting related to local frequencies in the application.properties file.

When executing the below command, java -jar exomiser-cli-11.0.0.jar -help

[julesjacobsen]

Now you've uncommented the exomiser.hg19.remm-path REMM is used for scoring non-coding variants, so unless you're running WGS samples you don't need it.

The error message is the same as your previous one - the program can't find the REMM file you specified as stated at the end of the WARN message line starting 2019-09-15 21:13:36.128 Is that file really there? If not you'll need to download it and put it there. You can find it here and you'll need both the gz and gz.tbi files

[gilskim]

Exomiser is now running correctly, after omitting exomiser.hg19.remm-path in application.properties file.

But, I've downloaded two files related to REMM file.

And, I have one more question related to the frequency files.

Could you tell me about setting for exomiser.hg19.local-frequency-path in in application.properties file, if I want to set several frequency files.

Is it possible to locate the downloaded frequency files to a specific path regardless of the file name or format.

Thank you for your time.

[julesjacobsen]

It will only accept one frequency file per genome assembly. The file can be located anywhere on the filesystem. It will need to be in a tabix indexed, tab delimited format #CHR POS REF ALT FREQ where freq is a percentage value.

[julesjacobsen]

@gilskim I presume this is closable? If you still have issues, please re-open.