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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 with Test run #497

Closed kiranpatil222 closed 1 year ago

kiranpatil222 commented 1 year ago

Hi,

I just installed latest version on Exomiser 13.2, and ran example/test-analysis-exome

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled.
2023-06-07 14:29:26.325 ERROR 618207 --- [           main] o.s.boot.SpringApplication               : Application run failed

java.lang.IllegalStateException: Failed to execute CommandLineRunner

have got above error, I have changed the data folder and its version to 2302

julesjacobsen commented 1 year ago

Please could you include the command you tried to run and the application.properties along with the rest of the error message.

kiranpatil222 commented 1 year ago

Hi I ran below command java -Xms2g -Xmx4g -jar exomiser-cli-13.2.0.jar --analysis examples/test-analysis-exome.yml

Error Log A Tool to Annotate and Prioritize Exome Variants v13.2.0

2023-07-05 14:27:51.127  INFO 61720 --- [           main] org.monarchinitiative.exomiser.cli.Main  : Starting Main using Java 14.0.2 on victor with PID 61720 (/data/shared/clinical/ExomeAnalysis/clinical/Scratch/Resources/exomiser/exomiser-cli-13.2.0/exomiser-cli-13.2.0.jar started by kiran.patil in /data/shared/clinical/ExomeAnalysis/clinical/Scratch/Resources/exomiser/exomiser-cli-13.2.0)
2023-07-05 14:27:51.129  INFO 61720 --- [           main] org.monarchinitiative.exomiser.cli.Main  : No active profile set, falling back to 1 default profile: "default"
2023-07-05 14:27:51.712  INFO 61720 --- [           main] o.m.exomiser.cli.config.MainConfig       : Exomiser home: /data/shared/clinical/ExomeAnalysis/clinical/Scratch/Resources/exomiser/exomiser-cli-13.2.0
2023-07-05 14:27:51.720  INFO 61720 --- [           main] o.m.exomiser.cli.config.MainConfig       : Root data source directory set to: /data/shared/clinical/ExomeAnalysis/clinical/Scratch/Resources/exomiser/exomiser-cli-13.2.0/data
2023-07-05 14:27:51.723  INFO 61720 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialising Jannovar data from /data/shared/clinical/ExomeAnalysis/clinical/Scratch/Resources/exomiser/exomiser-cli-13.2.0/data/2302_hg19/2302_hg19_transcripts_ensembl.ser
2023-07-05 14:27:52.734  INFO 61720 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialisation took 1.01 sec.
2023-07-05 14:27:53.324  INFO 61720 --- [           main] o.m.e.c.g.dao.VariantWhiteListLoader     : Loading variant whitelist from: /data/shared/clinical/ExomeAnalysis/clinical/Scratch/Resources/exomiser/exomiser-cli-13.2.0/data/2302_hg19/2302_hg19_clinvar_whitelist.tsv.gz
2023-07-05 14:27:53.601  INFO 61720 --- [           main] o.m.e.c.g.dao.VariantWhiteListLoader     : Loaded 180928 variants into whitelist
2023-07-05 14:27:54.362  INFO 61720 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialising Jannova
2023-07-05 14:27:54.757  INFO 61720 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialisation took 0.394 sec.
2023-07-05 14:27:54.908  INFO 61720 --- [           main] o.m.e.c.g.dao.VariantWhiteListLoader     : Loading variant whitelist from: /data/shared/clinical/ExomeAnalysis/clinical/Scratch/Resources/exomiser/exomiser-cli-13.2.0/data/2302_hg38/2302_hg38_clinvar_whitelist.tsv.gz
2023-07-05 14:27:55.092  INFO 61720 --- [           main] o.m.e.c.g.dao.VariantWhiteListLoader     : Loaded 180991 variants into whitelist
2023-07-05 14:27:55.255  INFO 61720 --- [           main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg19 genome analysis service
2023-07-05 14:27:55.255  INFO 61720 --- [           main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg38 genome analysis service
2023-07-05 14:27:56.373  INFO 61720 --- [           main] o.m.exomiser.cli.config.MainConfig       : Default results directory set to: /data/shared/clinical/ExomeAnalysis/clinical/Scratch/Resources/exomiser/exomiser-cli-13.2.0/results
2023-07-05 14:27:56.384  INFO 61720 --- [           main] o.m.e.a.ExomiserConfigReporter           : exomiser.data-directory: /data/shared/clinical/ExomeAnalysis/clinical/Scratch/Resources/exomiser/exomiser-cli-13.2.0/data/
2023-07-05 14:27:56.385  INFO 61720 --- [           main] o.m.e.a.ExomiserConfigReporter           : exomiser.hg19.data-version: 2302
2023-07-05 14:27:56.385  INFO 61720 --- [           main] o.m.e.a.ExomiserConfigReporter           : exomiser.hg38.data-version: 2302
2023-07-05 14:27:56.385  INFO 61720 --- [           main] o.m.e.a.ExomiserConfigReporter           : exomiser.phenotype.data-version: 2302
2023-07-05 14:27:56.493  INFO 61720 --- [           main] org.monarchinitiative.exomiser.cli.Main  : Started Main in 5.685 seconds (JVM running for 5.93)
2023-07-05 14:27:56.696  INFO 61720 --- [           main] o.m.e.cli.ExomiserCommandLineRunner      : Exomiser running...
2023-07-05 14:27:56.713  INFO 61720 --- [           main] o.m.exomiser.core.Exomiser               : Running analysis using hg38 assembly with mode: PASS_ONLY
2023-07-05 14:27:56.715  INFO 61720 --- [           main] o.m.e.c.analysis.AbstractAnalysisRunner  : Validating sample input data
2023-07-05 14:27:56.742  INFO 61720 --- [           main] o.m.e.core.model.SampleIdentifiers       : Proband sample name not specified - using sample name 'manuel' from VCF
2023-07-05 14:27:56.743  INFO 61720 --- [           main] o.m.e.c.a.s.PedigreeSampleValidator      : No pedigree provided for sample 'manuel'
2023-07-05 14:27:56.743  INFO 61720 --- [           main] o.m.e.c.a.s.PedigreeSampleValidator      : Creating single-sample pedigree for manuel
2023-07-05 14:27:56.749  INFO 61720 --- [           main] o.m.e.c.analysis.AbstractAnalysisRunner  : Running analysis for proband manuel (sample 1 in VCF) from samples: [manuel]. Using coordinates for genome assembly hg38.
2023-07-05 14:27:56.893  INFO 61720 --- [           main] o.m.e.c.analysis.AbstractAnalysisRunner  : Filtering variants with:
2023-07-05 14:27:56.893  INFO 61720 --- [           main] o.m.e.c.analysis.AbstractAnalysisRunner  : FailedVariantFilter{}
2023-07-05 14:27:56.893  INFO 61720 --- [           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]}
2023-07-05 14:27:56.894  INFO 61720 --- [           main] o.m.e.c.analysis.AbstractAnalysisRunner  : FrequencyFilter{maxFreq=2.0}
2023-07-05 14:27:56.895  INFO 61720 --- [           main] o.m.e.c.analysis.AbstractAnalysisRunner  : Wrapping FrequencyFilter{maxFreq=2.0} with VariantDataProvider for sources [THOUSAND_GENOMES, TOPMED, UK10K, ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, EXAC_EAST_ASIAN, EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, EXAC_OTHER, EXAC_SOUTH_ASIAN, GNOMAD_E_AFR, GNOMAD_E_AMR, GNOMAD_E_EAS, GNOMAD_E_FIN, GNOMAD_E_NFE, GNOMAD_E_OTH, GNOMAD_E_SAS, GNOMAD_G_AFR, GNOMAD_G_AMR, GNOMAD_G_EAS, GNOMAD_G_FIN, GNOMAD_G_NFE, GNOMAD_G_OTH, GNOMAD_G_SAS]
2023-07-05 14:27:56.895  INFO 61720 --- [           main] o.m.e.c.analysis.AbstractAnalysisRunner  : PathogenicityFilter{keepNonPathogenic=true}
2023-07-05 14:27:56.896  INFO 61720 --- [           main] o.m.e.c.analysis.AbstractAnalysisRunner  : Wrapping PathogenicityFilter{keepNonPathogenic=true} with VariantDataProvider for sources [REVEL, MVP]
2023-07-05 14:27:56.896  INFO 61720 --- [           main] o.m.e.core.genome.VariantFactoryImpl     : Annotating variant records, trimming sequences and normalising positions...
2023-07-05 14:27:57.356  INFO 61720 --- [           main] o.m.e.core.genome.VariantFactoryImpl     : Processed 3706 variant records into 3705 single allele variants (including 0 structural variants)
2023-07-05 14:27:57.356  INFO 61720 --- [           main] o.m.e.core.genome.VariantFactoryImpl     : Variant annotation finished in 0m 0s 459ms (459 ms)
2023-07-05 14:27:57.358  INFO 61720 --- [           main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled.
Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled.2023-07-05 14:27:57.356  INFO 61720 --- [           main] o.m.e.core.genome.VariantFactoryImpl     : Variant annotation finished in 0m 0s 459ms (459 ms)
2023-07-05 14:27:57.358  INFO 61720 --- [           main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled.
2023-07-05 14:27:57.371 ERROR 61720 --- [           main] o.s.boot.SpringApplication               : Application run failed

java.lang.IllegalStateException: Failed to execute CommandLineRunner
        at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:771)
        at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:752)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:314)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1303)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1292)
        at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53)
Caused by: org.monarchinitiative.svart.CoordinatesOutOfBoundsException: Fully-closed coordinates 1:249149660-249149661 out of contig bounds [1,248956422]
        at org.monarchinitiative.svart.Coordinates.validateCoordinates(Coordinates.java:197)
        at org.monarchinitiative.svart.BaseGenomicRegion.<init>(BaseGenomicRegion.java:23)
        at org.monarchinitiative.svart.BaseVariant.<init>(BaseVariant.java:20)
        at org.monarchinitiative.svart.impl.DefaultVariant.<init>(DefaultVariant.java:8)
        at org.monarchinitiative.svart.impl.DefaultVariant.of(DefaultVariant.java:23)
        at org.monarchinitiative.svart.Variant.of(Variant.java:85)
        at org.monarchinitiative.svart.util.VcfConverter.convert(VcfConverter.java:60)
        at org.monarchinitiative.exomiser.core.genome.VariantContextConverter.convertToVariant(VariantContextConverter.java:106)
        at org.monarchinitiative.exomiser.core.genome.VariantFactoryImpl.buildVariantEvaluations(VariantFactoryImpl.java:161)
        at org.monarchinitiative.exomiser.core.genome.VariantFactoryImpl.lambda$buildAlleleVariantEvaluations$1(VariantFactoryImpl.java:110)
        at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
        at java.base/java.util.ArrayList$SubList$2.forEachRemaining(ArrayList.java:1481)
        at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
        at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
        at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
        at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
        at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
        at java.base/java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:274)
        at java.base/java.util.stream.ReferencePipeline$11$1.accept(ReferencePipeline.java:442)
        at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
        at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
        at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
        at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
        at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913)
        at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578)
        at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.loadAndFilterVariants(AbstractAnalysisRunner.java:208)
        at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.run(AbstractAnalysisRunner.java:113)
        at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:83)
        at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:69)
        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:768)
        ... 5 common frames omitted
julesjacobsen commented 1 year ago

Ah, this error:

CoordinatesOutOfBoundsException: Fully-closed coordinates 1:249149660-249149661 out of contig bounds [1,248956422]

Is telling you that the coordinates of a variant in your input VCF 1:249149660-249149661 do not fit within the bounds of the contig [1,248956422] i.e. 249149660 > 248956422

Assembly chr1 length
GRCh37 249250621
GRCh38 248956422

This would fit on a GRCh37/hg19 chromosome 1 but not on a GRCh38/hg38 chromosome 1. Are you sure you've told Exomiser the correct assembly your input VCF was called on?

kiranpatil222 commented 1 year ago

Ohh Ya thanks a lot,, I had changed to hg38 after configuration So was that error, it ran perfectly after i made it to 19