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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
190 stars 54 forks source link

`java.nio.file.AccessDeniedException: /app/classes/results` / empty results #555

Closed matentzn closed 3 months ago

matentzn commented 3 months ago

I am trying to exomise:

docker run -it \
                -v "/Users/matentzn/Dropbox/health/exomiser_analysis/exomiser-data:/exomiser-data" \
                -v "/Users/matentzn/Dropbox/health/exomiser_analysis/exomiser-config/:/exomiser" \
                -v "/Users/matentzn/Dropbox/health/exomiser_analysis/exomiser-results:/results" \
                exomiser/exomiser-cli:14.0.0 \
                --sample /exomiser/x-phenopacket.yml \
                --analysis /exomiser/x-analysis.yml \
                --spring.config.location=/exomiser/application.properties

But the results dir is empty and I get an error which I can't quite understand:

java.nio.file.AccessDeniedException: /app/classes/results
        at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90) ~[na:na]
        at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106) ~[na:na]
        at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) ~[na:na]
Full log here ``` Welcome to: _____ _ _____ _ |_ _| |__ ___ | ____|_ _____ _ __ ___ (_)___ ___ _ __ | | | '_ \ / _ \ | _| \ \/ / _ \| '_ ` _ \| / __|/ _ \ '__| | | | | | | __/ | |___ > < (_) | | | | | | \__ \ __/ | |_| |_| |_|\___| |_____/_/\_\___/|_| |_| |_|_|___/\___|_| A Tool to Annotate and Prioritize Exome Variants v14.0.0 2024-03-24T13:04:29.647Z INFO 1 --- [ main] o.monarchinitiative.exomiser.cli.Main : Starting Main using Java 17.0.6 with PID 1 (/app/classes started by nonroot in /home/nonroot) 2024-03-24T13:04:29.650Z INFO 1 --- [ main] o.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to 1 default profile: "default" 2024-03-24T13:04:30.091Z INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /app/classes 2024-03-24T13:04:30.098Z INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /exomiser-data 2024-03-24T13:04:30.100Z INFO 1 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /exomiser-data/2402_hg19/2402_hg19_transcripts_ensembl.ser 2024-03-24T13:04:30.662Z INFO 1 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 0.561 sec. 2024-03-24T13:04:31.108Z INFO 1 --- [ main] o.m.e.c.g.dao.ClinVarWhiteListReader : Reading ClinVar whitelist... 2024-03-24T13:04:31.112Z INFO 1 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'clinvar' opened with 2353837 entries 2024-03-24T13:04:32.216Z INFO 1 --- [ main] o.m.e.c.g.dao.ClinVarWhiteListReader : Read 203570 ClinVar whitelist variants in 1108 ms 2024-03-24T13:04:32.229Z INFO 1 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Loaded 203570 whitelist variants 2024-03-24T13:04:32.281Z INFO 1 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'alleles' opened with 826441620 entries 2024-03-24T13:04:32.292Z INFO 1 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'clinvar' opened with 2353837 entries 2024-03-24T13:04:32.618Z INFO 1 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg19 genome analysis service 2024-03-24T13:04:33.241Z ERROR 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Unable to create default output directory for results /app/classes/results java.nio.file.AccessDeniedException: /app/classes/results at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90) ~[na:na] at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106) ~[na:na] at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) ~[na:na] at java.base/sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:397) ~[na:na] at java.base/java.nio.file.Files.createDirectory(Files.java:700) ~[na:na] at org.monarchinitiative.exomiser.cli.config.MainConfig.resultsDir(MainConfig.java:66) ~[classes/:na] at org.monarchinitiative.exomiser.cli.config.MainConfig$$SpringCGLIB$$0.CGLIB$resultsDir$1() ~[classes/:na] at org.monarchinitiative.exomiser.cli.config.MainConfig$$SpringCGLIB$$FastClass$$1.invoke() ~[classes/:na] at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:258) ~[spring-core-6.1.4.jar:6.1.4] at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:331) ~[spring-context-6.1.4.jar:6.1.4] at org.monarchinitiative.exomiser.cli.config.MainConfig$$SpringCGLIB$$0.resultsDir() ~[classes/:na] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) ~[na:na] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na] at java.base/java.lang.reflect.Method.invoke(Method.java:568) ~[na:na] at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:140) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:647) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:639) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1335) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1165) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:325) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:323) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:975) ~[spring-beans-6.1.4.jar:6.1.4] at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:959) ~[spring-context-6.1.4.jar:6.1.4] at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:624) ~[spring-context-6.1.4.jar:6.1.4] at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:754) ~[spring-boot-3.2.3.jar:3.2.3] at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:456) ~[spring-boot-3.2.3.jar:3.2.3] at org.springframework.boot.SpringApplication.run(SpringApplication.java:334) ~[spring-boot-3.2.3.jar:3.2.3] at org.springframework.boot.SpringApplication.run(SpringApplication.java:1354) ~[spring-boot-3.2.3.jar:3.2.3] at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343) ~[spring-boot-3.2.3.jar:3.2.3] at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53) ~[classes/:na] 2024-03-24T13:04:33.242Z INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: /app/classes/results 2024-03-24T13:04:33.250Z INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.data-directory: /exomiser-data 2024-03-24T13:04:33.250Z INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg19.data-version: 2402 2024-03-24T13:04:33.250Z INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg19.clinvar-data-version: 2402 2024-03-24T13:04:33.250Z INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg38.data-version: - 2024-03-24T13:04:33.250Z INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.phenotype.data-version: 2402 2024-03-24T13:04:33.350Z INFO 1 --- [ main] o.monarchinitiative.exomiser.cli.Main : Started Main in 3.935 seconds (process running for 4.103) 2024-03-24T13:04:33.518Z INFO 1 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Exomiser running... 2024-03-24T13:04:33.528Z INFO 1 --- [ main] o.m.exomiser.core.Exomiser : Running analysis using hg19 assembly with mode: PASS_ONLY 2024-03-24T13:04:33.530Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Validating sample input data 2024-03-24T13:04:33.551Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running analysis for proband 23ES_427 (sample 1 in VCF) from samples: [23ES_427]. Using coordinates for genome assembly hg19. 2024-03-24T13:04:33.687Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Filtering variants with: 2024-03-24T13:04:33.688Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FailedVariantFilter{} 2024-03-24T13:04:33.688Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : VariantEffectFilter{offTargetVariantTypes=[CODING_TRANSCRIPT_INTRON_VARIANT, FIVE_PRIME_UTR_EXON_VARIANT, THREE_PRIME_UTR_EXON_VARIANT, FIVE_PRIME_UTR_INTRON_VARIANT, THREE_PRIME_UTR_INTRON_VARIANT, NON_CODING_TRANSCRIPT_EXON_VARIANT, NON_CODING_TRANSCRIPT_INTRON_VARIANT, UPSTREAM_GENE_VARIANT, DOWNSTREAM_GENE_VARIANT, INTERGENIC_VARIANT, REGULATORY_REGION_VARIANT]} 2024-03-24T13:04:33.688Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FrequencyFilter{maxFreq=2.0} 2024-03-24T13:04:33.689Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Wrapping FrequencyFilter{maxFreq=2.0} with VariantDataProvider for sources [UK10K, GNOMAD_E_AFR, GNOMAD_E_AMR, GNOMAD_E_EAS, GNOMAD_E_NFE, GNOMAD_E_SAS, GNOMAD_G_AFR, GNOMAD_G_AMR, GNOMAD_G_EAS, GNOMAD_G_NFE, GNOMAD_G_SAS] 2024-03-24T13:04:33.689Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PathogenicityFilter{keepNonPathogenic=true} 2024-03-24T13:04:33.689Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Wrapping PathogenicityFilter{keepNonPathogenic=true} with VariantDataProvider for sources [REVEL, MVP] 2024-03-24T13:04:33.690Z INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Annotating variant records, trimming sequences and normalising positions... 2024-03-24T13:04:41.541Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 100000 variants - 1073 passed variant filters... 2024-03-24T13:04:43.379Z INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Processed 148233 variant records into 125975 single allele variants (including 0 structural variants), 1149 are missing annotations, most likely due to non-numeric chromosome designations 2024-03-24T13:04:43.380Z INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Variant annotation finished in 0m 9s 689ms (9689 ms) 2024-03-24T13:04:43.380Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 127124 variants - 1373 passed variant filters 2024-03-24T13:04:43.385Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Checking inheritance mode compatibility with [AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_RECESSIVE, X_DOMINANT, MITOCHONDRIAL] for genes which passed filters 2024-03-24T13:04:43.430Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running GeneFilter: InheritanceFilter{compatibleModes=[AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_RECESSIVE, X_DOMINANT, MITOCHONDRIAL]} 2024-03-24T13:04:43.443Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: OmimPrioritiser{} 2024-03-24T13:04:43.838Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: HiPhivePriority{options=HiPhiveOptions{diseaseId='', candidateGeneSymbol='', benchmarkingEnabled=false, runPpi=true, runHuman=true, runMouse=true, runFish=true}} 2024-03-24T13:04:45.076Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Variant filter stats are: 2024-03-24T13:04:45.076Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FAILED_VARIANT_FILTER: pass=125975 fail=0 2024-03-24T13:04:45.076Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : VARIANT_EFFECT_FILTER: pass=27780 fail=98195 2024-03-24T13:04:45.076Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FREQUENCY_FILTER: pass=1373 fail=26407 2024-03-24T13:04:45.076Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PATHOGENICITY_FILTER: pass=1373 fail=0 2024-03-24T13:04:45.076Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : INHERITANCE_FILTER: pass=867 fail=506 2024-03-24T13:04:46.144Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Scoring genes 2024-03-24T13:04:46.433Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Analysed sample 23ES_427 with 562 genes containing 867 filtered variants 2024-03-24T13:04:46.433Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Finished analysis in 0m 12s 882ms (12882 ms) 2024-03-24T13:04:46.433Z INFO 1 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Writing results... 2024-03-24T13:04:47.321Z INFO 1 --- [ main] o.monarchinitiative.exomiser.cli.Main : Exomising finished - Bye! ```

Any help much appreciated.

matentzn commented 3 months ago

I got the docker instructions from your tutorial.

If I change the results dir:

docker run -it \
        -v "$(PWD)/exomiser-data:/exomiser-data" \
        -v "$(PWD)/exomiser-config/:/exomiser" \
        -v "$(PWD)/exomiser-results:/app/classes/results" \
        exomiser/exomiser-cli:14.0.0 \
        --sample /exomiser/x-phenopacket.yml \
        --analysis /exomiser/x-analysis.yml \
        --spring.config.location=/exomiser/application.properties

The error is not thrown, but still, no results are generated.

Full log ``` A Tool to Annotate and Prioritize Exome Variants v14.0.0 2024-03-24T13:11:48.394Z INFO 1 --- [ main] o.monarchinitiative.exomiser.cli.Main : Starting Main using Java 17.0.6 with PID 1 (/app/classes started by nonroot in /home/nonroot) 2024-03-24T13:11:48.396Z INFO 1 --- [ main] o.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to 1 default profile: "default" 2024-03-24T13:11:48.892Z INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /app/classes 2024-03-24T13:11:48.900Z INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /exomiser-data 2024-03-24T13:11:48.902Z INFO 1 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /exomiser-data/2402_hg19/2402_hg19_transcripts_ensembl.ser 2024-03-24T13:11:49.635Z INFO 1 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 0.732 sec. 2024-03-24T13:11:50.215Z INFO 1 --- [ main] o.m.e.c.g.dao.ClinVarWhiteListReader : Reading ClinVar whitelist... 2024-03-24T13:11:50.220Z INFO 1 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'clinvar' opened with 2353837 entries 2024-03-24T13:11:52.028Z INFO 1 --- [ main] o.m.e.c.g.dao.ClinVarWhiteListReader : Read 203570 ClinVar whitelist variants in 1812 ms 2024-03-24T13:11:52.051Z INFO 1 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Loaded 203570 whitelist variants 2024-03-24T13:11:52.117Z INFO 1 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'alleles' opened with 826441620 entries 2024-03-24T13:11:52.129Z INFO 1 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'clinvar' opened with 2353837 entries 2024-03-24T13:11:52.557Z INFO 1 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg19 genome analysis service 2024-03-24T13:11:53.334Z INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: /app/classes/results 2024-03-24T13:11:53.343Z INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.data-directory: /exomiser-data 2024-03-24T13:11:53.343Z INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg19.data-version: 2402 2024-03-24T13:11:53.343Z INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg19.clinvar-data-version: 2402 2024-03-24T13:11:53.343Z INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg38.data-version: - 2024-03-24T13:11:53.343Z INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.phenotype.data-version: 2402 2024-03-24T13:11:53.437Z INFO 1 --- [ main] o.monarchinitiative.exomiser.cli.Main : Started Main in 5.247 seconds (process running for 5.454) 2024-03-24T13:11:53.607Z INFO 1 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Exomiser running... 2024-03-24T13:11:53.615Z INFO 1 --- [ main] o.m.exomiser.core.Exomiser : Running analysis using hg19 assembly with mode: PASS_ONLY 2024-03-24T13:11:53.618Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Validating sample input data 2024-03-24T13:11:53.641Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running analysis for proband 23ES_427 (sample 1 in VCF) from samples: [23ES_427]. Using coordinates for genome assembly hg19. 2024-03-24T13:11:53.845Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Filtering variants with: 2024-03-24T13:11:53.845Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FailedVariantFilter{} 2024-03-24T13:11:53.845Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : VariantEffectFilter{offTargetVariantTypes=[CODING_TRANSCRIPT_INTRON_VARIANT, FIVE_PRIME_UTR_EXON_VARIANT, THREE_PRIME_UTR_EXON_VARIANT, FIVE_PRIME_UTR_INTRON_VARIANT, THREE_PRIME_UTR_INTRON_VARIANT, NON_CODING_TRANSCRIPT_EXON_VARIANT, NON_CODING_TRANSCRIPT_INTRON_VARIANT, UPSTREAM_GENE_VARIANT, DOWNSTREAM_GENE_VARIANT, INTERGENIC_VARIANT, REGULATORY_REGION_VARIANT]} 2024-03-24T13:11:53.846Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FrequencyFilter{maxFreq=2.0} 2024-03-24T13:11:53.846Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Wrapping FrequencyFilter{maxFreq=2.0} with VariantDataProvider for sources [UK10K, GNOMAD_E_AFR, GNOMAD_E_AMR, GNOMAD_E_EAS, GNOMAD_E_NFE, GNOMAD_E_SAS, GNOMAD_G_AFR, GNOMAD_G_AMR, GNOMAD_G_EAS, GNOMAD_G_NFE, GNOMAD_G_SAS] 2024-03-24T13:11:53.847Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PathogenicityFilter{keepNonPathogenic=true} 2024-03-24T13:11:53.847Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Wrapping PathogenicityFilter{keepNonPathogenic=true} with VariantDataProvider for sources [REVEL, MVP] 2024-03-24T13:11:53.847Z INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Annotating variant records, trimming sequences and normalising positions... 2024-03-24T13:12:01.718Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 100000 variants - 1073 passed variant filters... 2024-03-24T13:12:03.654Z INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Processed 148233 variant records into 125975 single allele variants (including 0 structural variants), 1149 are missing annotations, most likely due to non-numeric chromosome designations 2024-03-24T13:12:03.655Z INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Variant annotation finished in 0m 9s 806ms (9806 ms) 2024-03-24T13:12:03.655Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 127124 variants - 1373 passed variant filters 2024-03-24T13:12:03.660Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Checking inheritance mode compatibility with [AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_RECESSIVE, X_DOMINANT, MITOCHONDRIAL] for genes which passed filters 2024-03-24T13:12:03.704Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running GeneFilter: InheritanceFilter{compatibleModes=[AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_RECESSIVE, X_DOMINANT, MITOCHONDRIAL]} 2024-03-24T13:12:03.716Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: OmimPrioritiser{} 2024-03-24T13:12:04.222Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: HiPhivePriority{options=HiPhiveOptions{diseaseId='', candidateGeneSymbol='', benchmarkingEnabled=false, runPpi=true, runHuman=true, runMouse=true, runFish=true}} 2024-03-24T13:12:05.405Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Variant filter stats are: 2024-03-24T13:12:05.405Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FAILED_VARIANT_FILTER: pass=125975 fail=0 2024-03-24T13:12:05.405Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : VARIANT_EFFECT_FILTER: pass=27780 fail=98195 2024-03-24T13:12:05.405Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FREQUENCY_FILTER: pass=1373 fail=26407 2024-03-24T13:12:05.405Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PATHOGENICITY_FILTER: pass=1373 fail=0 2024-03-24T13:12:05.405Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : INHERITANCE_FILTER: pass=867 fail=506 2024-03-24T13:12:06.504Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Scoring genes 2024-03-24T13:12:06.782Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Analysed sample 23ES_427 with 562 genes containing 867 filtered variants 2024-03-24T13:12:06.783Z INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Finished analysis in 0m 13s 141ms (13141 ms) 2024-03-24T13:12:06.783Z INFO 1 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Writing results... 2024-03-24T13:12:07.721Z INFO 1 --- [ main] o.monarchinitiative.exomiser.cli.Main : Exomising finished - Bye! ```
lpsyy commented 3 months ago

in the first section, the program prompts “java.nio.file.AccessDeniedException: /app/classes/results”，maybe the file permission should change.

matentzn commented 3 months ago

Thanks @lpsyy the error is gone now but the results dir remains empty!

matentzn commented 3 months ago

@yaseminbridges sorted it out for me! I was missing the --output-dir option!

docker run -it \
                -v "/Users/matentzn/Dropbox/health/exomiser_analysis/exomiser-data:/exomiser-data" \
                -v "/Users/matentzn/Dropbox/health/exomiser_analysis/exomiser-config/:/exomiser" \
                -v "/Users/matentzn/Dropbox/health/exomiser_analysis/exomiser-results:/results" \
                exomiser/exomiser-cli:14.0.0 \
                --sample /exomiser/x-phenopacket.yml \
                --analysis /exomiser/x-analysis.yml \
                --output-directory /results \
                --spring.config.location=/exomiser/application.properties

Thanks all!