Error while running test-analysis-exome.yml #589
Comments
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Have you checked that you're analysing the VCF using the correct genome build? You have Exomiser set up to work on hg38 but it threw an error with the cause: Given the lengths of chromosome 1 are defined like so for GRCh37 and GRCh38: It suggests you are trying to analyse a VCF called on GRCh37 using data from GRCh38. This will not produce good results... Double-check your input data and Exomiser setup data are for the same assembly. In this case your |
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Thank you very much. That solved the problem! |
Hi,
Thank you for providing this useful software for the scientific community.
It's been installed on our HPC systems in NIH for years. I am in the process of updating to version 14.1.0 and ran into the following error.
The test-analysis-exome.yml in examples directory was modified from hg19 to hg38 and nothing else was changed.
$ ls -l /.../data/2406_hg38/*
-rwxrwxr-x Jun 13 2024 /fdb/exomiser/data/2406_hg38/2406_hg38_clinvar.mv.db*
-rwxrwxr-x Jun 10 2024 /fdb/exomiser/data/2406_hg38/2406_hg38_genome.mv.db*
-rwxrwxr-x Jun 10 2024 /fdb/exomiser/data/2406_hg38/2406_hg38_transcripts_ensembl.ser*
-rwxrwxr-x Jun 10 2024 /fdb/exomiser/data/2406_hg38/2406_hg38_transcripts_refseq.ser*
-rwxrwxr-x 74M Jun 10 2024 /fdb/exomiser/data/2406_hg38/2406_hg38_transcripts_ucsc.ser*
-rwxrwxr-x 30G Jun 10 2024 /fdb/exomiser/data/2406_hg38/2406_hg38_variants.mv.db*
$ ls -l /..../data/cadd/1.7/hg38/
total 83G
-rw-r--r-- 1 1.2G Jan 11 2024 gnomad.genomes.r4.0.indel.tsv.gz
-rw-r--r-- 1 1.9M Jan 11 2024 gnomad.genomes.r4.0.indel.tsv.gz.tbi
-rw-r--r-- 1 82G Jan 29 2024 whole_genome_SNVs.tsv.gz
-rw-r--r-- 1 2.7M Jan 29 2024 whole_genome_SNVs.tsv.gz.tbi
$ ls -l /..../data/remm/0.3.1.post1/
total 28G
-rw-r--r-- 1 2G Jan 29 11:34 ReMM.v0.3.1.post1.hg19.tsv.gz
-rw-r--r-- 1 2.4M Jan 29 11:34 ReMM.v0.3.1.post1.hg19.tsv.gz.tbi
-rw-r--r-- 1 17G Jan 29 11:42 ReMM.v0.3.1.post1.hg38.tsv.gz
-rw-r--r-- 1 2.7M Jan 29 11:42 ReMM.v0.3.1.post1.hg38.tsv.gz.tbi
-rw-r--r-- 1 264 Jan 29 11:42 ReMM.v0.3.1.post1.md5
$ cat applications.properties
exomiser.data-directory=/fdb/exomiser/data/
remm.version=0.3.1.post1
cadd.version=1.7
#### hg38 assembly
exomiser.hg38.data-version=2406
exomiser.hg38.cadd-snv-path=${exomiser.data-directory}/cadd/${cadd.version}/hg38/whole_genome_SNVs.tsv.gz
exomiser.hg38.cadd-in-del-path=${exomiser.data-directory}/cadd/${cadd.version}/hg38/gnomad.genomes.r4.0.indel.tsv.gz
exomiser.hg38.remm-path=${exomiser.data-directory}/remm/${remm.version}/ReMM.v${remm.version}.hg38.tsv.gz
exomiser.hg38.clinvar-data-version=2406
### phenotypes ###
exomiser.phenotype.data-version=2406
exomiser.phenotype.data-directory=${exomiser.data-directory}/${exomiser.phenotype.data-version}_phenotype
exomiser.phenotype.random-walk-file-name=rw_string_10.mv
### caching ###
spring.cache.type=caffeine
spring.cache.caffeine.spec=maximumSize=480000
### logging ###
logging.file-output
logging.level.com.zaxxer.hikari=ERROR
Then I ran:
$ java -Xms2g -Xmx48g -jar exomiser-cli-14.1.0.jar --analysis examples/test-analysis-exome.yml
Welcome to:
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| | | | | | / | |_ > < () | | | | | | _ \ / |
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A Tool to Annotate and Prioritize Exome Variants v14.1.0
2025-01-30T15:50:43.284-05:00 INFO 138646 --- [ main] o.monarchinitiative.exomiser.cli.Main : Starting Main using Java 17.0.3.1 with PID 138646 (/usr/local/apps/exomiser/14.1.0/exomiser-cli-14.1.0.jar started by maoj in /usr/local/apps/exomiser/14.1.0)
2025-01-30T15:50:43.287-05:00 INFO 138646 --- [ main] o.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to 1 default profile: "default"
2025-01-30T15:50:43.769-05:00 INFO 138646 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /usr/local/apps/exomiser/14.1.0
2025-01-30T15:50:43.777-05:00 INFO 138646 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /fdb/exomiser/data
2025-01-30T15:50:43.779-05:00 INFO 138646 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /fdb/exomiser/data/2406_hg38/2406_hg38_transcripts_ensembl.ser
2025-01-30T15:50:44.179-05:00 INFO 138646 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 0.398 sec.
2025-01-30T15:50:45.814-05:00 INFO 138646 --- [ main] o.m.e.c.g.dao.ClinVarWhiteListReader : Reading ClinVar whitelist...
2025-01-30T15:50:45.820-05:00 INFO 138646 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'clinvar' opened with 2897469 entries
2025-01-30T15:50:47.796-05:00 INFO 138646 --- [ main] o.m.e.c.g.dao.ClinVarWhiteListReader : Read 238630 ClinVar whitelist variants in 1981 ms
2025-01-30T15:50:47.820-05:00 INFO 138646 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Loaded 238630 whitelist variants
2025-01-30T15:50:47.870-05:00 INFO 138646 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Opening CADD snv data from source: /fdb/exomiser/data/cadd/1.7/hg38/whole_genome_SNVs.tsv.gz
2025-01-30T15:50:47.927-05:00 INFO 138646 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Opening CADD InDel data from source: /fdb/exomiser/data/cadd/1.7/hg38/gnomad.genomes.r4.0.indel.tsv.gz
2025-01-30T15:50:47.956-05:00 INFO 138646 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Opening REMM data from source: /fdb/exomiser/data/remm/0.3.1.post1/ReMM.v0.3.1.post1.hg38.tsv.gz
2025-01-30T15:50:48.076-05:00 INFO 138646 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'alleles' opened with 816467174 entries
2025-01-30T15:50:48.092-05:00 INFO 138646 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'clinvar' opened with 2897469 entries
2025-01-30T15:50:49.595-05:00 INFO 138646 --- [ main] o.m.e.core.genome.dao.ClinVarDaoMvStore : Created 18551 ClinVar gene stats in 1502 ms
2025-01-30T15:50:49.932-05:00 INFO 138646 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg38 genome analysis service
2025-01-30T15:50:53.242-05:00 INFO 138646 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: /usr/local/apps/exomiser/14.1.0/results
2025-01-30T15:50:53.259-05:00 INFO 138646 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.data-directory: /fdb/exomiser/data/
2025-01-30T15:50:53.259-05:00 INFO 138646 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg19.data-version: -
2025-01-30T15:50:53.259-05:00 INFO 138646 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg38.data-version: 2406
2025-01-30T15:50:53.259-05:00 INFO 138646 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg38.clinvar-data-version: 2406
2025-01-30T15:50:53.259-05:00 INFO 138646 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.phenotype.data-version: 2406
2025-01-30T15:50:53.259-05:00 INFO 138646 --- [ main] o.m.e.a.ExomiserConfigReporter : spring.cache.type: caffeine
2025-01-30T15:50:53.403-05:00 INFO 138646 --- [ main] o.monarchinitiative.exomiser.cli.Main : Started Main in 10.326 seconds (process running for 10.521)
2025-01-30T15:50:53.544-05:00 INFO 138646 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Exomiser running...
2025-01-30T15:50:53.554-05:00 INFO 138646 --- [ main] o.m.exomiser.core.Exomiser : Running analysis using hg38 assembly with mode: PASS_ONLY
2025-01-30T15:50:53.557-05:00 INFO 138646 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Validating sample input data
2025-01-30T15:50:53.588-05:00 INFO 138646 --- [ main] o.m.e.core.model.SampleIdentifiers : Proband sample name not specified - using sample name 'manuel' from VCF
2025-01-30T15:50:53.588-05:00 INFO 138646 --- [ main] o.m.e.c.a.s.PedigreeSampleValidator : No pedigree provided for sample 'manuel'
2025-01-30T15:50:53.588-05:00 INFO 138646 --- [ main] o.m.e.c.a.s.PedigreeSampleValidator : Creating single-sample pedigree for manuel
2025-01-30T15:50:53.593-05:00 INFO 138646 --- [ 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.
2025-01-30T15:50:53.714-05:00 INFO 138646 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Filtering variants with:
2025-01-30T15:50:53.715-05:00 INFO 138646 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FailedVariantFilter{}
2025-01-30T15:50:53.715-05:00 INFO 138646 --- [ 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]}
2025-01-30T15:50:53.715-05:00 INFO 138646 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FrequencyFilter{maxFreq=2.0}
2025-01-30T15:50:53.716-05:00 INFO 138646 --- [ 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]
2025-01-30T15:50:53.716-05:00 INFO 138646 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PathogenicityFilter{keepNonPathogenic=true}
2025-01-30T15:50:53.717-05:00 INFO 138646 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Wrapping PathogenicityFilter{keepNonPathogenic=true} with VariantDataProvider for sources [REVEL, MVP]
2025-01-30T15:50:53.717-05:00 INFO 138646 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Annotating variant records, trimming sequences and normalising positions...
2025-01-30T15:50:54.404-05:00 INFO 138646 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Processed 3706 variant records into 3705 single allele variants (including 0 structural variants)
2025-01-30T15:50:54.404-05:00 INFO 138646 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Variant annotation finished in 0m 0s 686ms (686 ms)
2025-01-30T15:50:54.406-05:00 INFO 138646 --- [ main] .s.b.a.l.ConditionEvaluationReportLogger :
Error starting ApplicationContext. To display the condition evaluation report re-run your application with 'debug' enabled.
2025-01-30T15:50:54.416-05:00 ERROR 138646 --- [ main] o.s.boot.SpringApplication : Application run failed
org.monarchinitiative.svart.CoordinatesOutOfBoundsException: One-based coordinates 1:249149660-249149661 out of contig bounds [1,248956422]
at org.monarchinitiative.svart.GenomicInterval.validateCoordinatesOnContig(GenomicInterval.java:48) ~[svart-2.0.0-RC6.jar:na]
at org.monarchinitiative.svart.BaseGenomicRegion.(BaseGenomicRegion.java:19) ~[svart-2.0.0-RC6.jar:na]
at org.monarchinitiative.svart.BaseGenomicVariant.(BaseGenomicVariant.java:23) ~[svart-2.0.0-RC6.jar:na]
at org.monarchinitiative.svart.impl.DefaultGenomicVariant.(DefaultGenomicVariant.java:8) ~[svart-2.0.0-RC6.jar:na]
at org.monarchinitiative.svart.impl.DefaultGenomicVariant.of(DefaultGenomicVariant.java:31) ~[svart-2.0.0-RC6.jar:na]
at org.monarchinitiative.svart.GenomicVariant.of(GenomicVariant.java:144) ~[svart-2.0.0-RC6.jar:na]
at org.monarchinitiative.svart.util.VcfConverter.convert(VcfConverter.java:75) ~[svart-2.0.0-RC6.jar:na]
at org.monarchinitiative.exomiser.core.genome.VariantContextConverter.convertToVariant(VariantContextConverter.java:113) ~[exomiser-core-14.1.0.jar:na]
at org.monarchinitiative.exomiser.core.genome.VariantFactoryImpl.buildVariantEvaluations(VariantFactoryImpl.java:161) ~[exomiser-core-14.1.0.jar:na]
at org.monarchinitiative.exomiser.core.genome.VariantFactoryImpl.lambda$buildAlleleVariantEvaluations$1(VariantFactoryImpl.java:110) ~[exomiser-core-14.1.0.jar:na]
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197) ~[na:na]
at java.base/java.util.ArrayList$SubList$2.forEachRemaining(ArrayList.java:1481) ~[na:na]
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509) ~[na:na]
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499) ~[na:na]
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150) ~[na:na]
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173) ~[na:na]
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) ~[na:na]
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596) ~[na:na]
at java.base/java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:276) ~[na:na]
at java.base/java.util.stream.ReferencePipeline$15$1.accept(ReferencePipeline.java:541) ~[na:na]
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133) ~[na:na]
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845) ~[na:na]
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509) ~[na:na]
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499) ~[na:na]
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:575) ~[na:na]
at java.base/java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260) ~[na:na]
at java.base/java.util.stream.ReferencePipeline.toArray(ReferencePipeline.java:616) ~[na:na]
at java.base/java.util.stream.ReferencePipeline.toArray(ReferencePipeline.java:622) ~[na:na]
at java.base/java.util.stream.ReferencePipeline.toList(ReferencePipeline.java:627) ~[na:na]
at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.loadAndFilterVariants(AbstractAnalysisRunner.java:235) ~[exomiser-core-14.1.0.jar:na]
at org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.run(AbstractAnalysisRunner.java:112) ~[exomiser-core-14.1.0.jar:na]
at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:83) ~[exomiser-core-14.1.0.jar:na]
at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:69) ~[exomiser-core-14.1.0.jar:na]
at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJob(ExomiserCommandLineRunner.java:90) ~[exomiser-cli-14.1.0.jar:na]
at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJobs(ExomiserCommandLineRunner.java:65) ~[exomiser-cli-14.1.0.jar:na]
at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.run(ExomiserCommandLineRunner.java:60) ~[exomiser-cli-14.1.0.jar:na]
at org.springframework.boot.SpringApplication.lambda$callRunner$5(SpringApplication.java:790) ~[spring-boot-3.2.3.jar:3.2.3]
at org.springframework.util.function.ThrowingConsumer$1.acceptWithException(ThrowingConsumer.java:83) ~[spring-core-6.1.4.jar:6.1.4]
at org.springframework.util.function.ThrowingConsumer.accept(ThrowingConsumer.java:60) ~[spring-core-6.1.4.jar:6.1.4]
at org.springframework.util.function.ThrowingConsumer$1.accept(ThrowingConsumer.java:88) ~[spring-core-6.1.4.jar:6.1.4]
at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:798) ~[spring-boot-3.2.3.jar:3.2.3]
at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:789) ~[spring-boot-3.2.3.jar:3.2.3]
at org.springframework.boot.SpringApplication.lambda$callRunners$3(SpringApplication.java:774) ~[spring-boot-3.2.3.jar:3.2.3]
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183) ~[na:na]
at java.base/java.util.stream.SortedOps$SizedRefSortingSink.end(SortedOps.java:357) ~[na:na]
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:510) ~[na:na]
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499) ~[na:na]
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150) ~[na:na]
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173) ~[na:na]
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) ~[na:na]
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596) ~[na:na]
at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:774) ~[spring-boot-3.2.3.jar:3.2.3]
at org.springframework.boot.SpringApplication.run(SpringApplication.java:341) ~[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) ~[exomiser-cli-14.1.0.jar:na]
Did I miss something? Thank you very much for your help.
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