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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 running exsomiser: Error starting ApplicationContext #428

Closed rhassnan closed 2 years ago

rhassnan commented 2 years ago

I am trying to run exomiser analysis using the test-analysis-exome.yml. It works fine when I use the example provided by Exomiser but when I use my own VCF files it produces this error:

2022-03-17 10:30:46.555 INFO 116268 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Annotating variant records, trimming sequences and normalising positions... 2022-03-17 10:30:50.975 INFO 116268 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 100000 variants - 1627 passed variant filters... 2022-03-17 10:30:54.106 INFO 116268 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Processed 191948 variant records into 192294 single allele variants (including 0 structural variants) 2022-03-17 10:30:54.106 INFO 116268 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Variant annotation finished in 0m 7s 550ms (7550 ms) 2022-03-17 10:30:54.107 INFO 116268 --- [ main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled. 2022-03-17 10:30:54.114 ERROR 116268 --- [ 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:52) Caused by: org.monarchinitiative.svart.CoordinatesOutOfBoundsException: Fully-closed coordinates 3:198023180-198023180 out of contig bounds [1,198022430] at org.monarchinitiative.svart.Coordinates.validateCoordinates(Coordinates.java:197) at org.monarchinitiative.svart.BaseGenomicRegion.(BaseGenomicRegion.java:23) at org.monarchinitiative.svart.BaseVariant.(BaseVariant.java:20) at org.monarchinitiative.svart.impl.DefaultVariant.(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$1.accept(ReferencePipeline.java:197) at java.base/java.util.ArrayList$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:596) at java.base/java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:276) at java.base/java.util.stream.ReferencePipeline$15$1.accept(ReferencePipeline.java:541) at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133) at java.base/java.util.Spliterators$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:682) at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.loadAndFilterVariants(AbstractAnalysisRunner.java:197) 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:791) ... 5 common frames omitted

Can someone help me with this error ? Thank you

ielis commented 2 years ago

Hi @rhassnan, the line 

Caused by: org.monarchinitiative.svart.CoordinatesOutOfBoundsException: Fully-closed coordinates 3:198023180-198023180 out of contig bounds [1,198022430]

indicates that your input VCF has a variant located at position 3:198,023,180.

However, contig 3 of the genomic assembly that you're working with (I'm assuming it's GRCh37) is only 198,022,430 bases long (check here).

So it seems like there is error in your input VCF where a variant is located past end of the contig.

rhassnan commented 2 years ago

Hi @ielis Thank you I changed the genomic assembly to hg38 and it working now. Thank you for helping !