Error: Contig chr1 does not have a length field.

[bsmith030465]

Hi,

I was trying to run exomiser on a sample, but get an error:

` . . 2020-09-30 10:09:47.973 INFO 5772 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Processed 6604493 variant records into 1818288 single allele variants, 7252 are missing annotations, most likely due to non-numeric chromosome designations 2020-09-30 10:09:47.973 INFO 5772 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Variant annotation finished in 15m 31s 935ms (931935 ms) 2020-09-30 10:09:47.974 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1825540 variants - 1595 passed variant filters 2020-09-30 10:09:47.998 INFO 5772 --- [ 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 2020-09-30 10:09:48.500 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running GeneFilter: InheritanceFilter{compatibleModes=[AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_RECESSIVE, X_DOMINANT, MITOCHONDRIAL]}2020-09-30 10:09:48.569 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: OmimPrioritiser{} 2020-09-30 10:09:51.679 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: HiPhivePriority{options=HiPhiveOptions{diseaseId='', candidateGeneSymbol='', benchmarkingEnabled=false, runPpi=true, runHuman=true, runMouse=true, runFish=true}} 2020-09-30 10:09:51.685 WARN 5772 --- [ main] o.m.e.c.phenotype.service.HpoIdChecker : Input HP:0032929 - unable to find current id. Returning input HP:0032929 2020-09-30 10:09:55.373 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Scoring genes 2020-09-30 10:09:55.513 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Analysed 689 genes containing 1076 filtered variants 2020-09-30 10:09:55.514 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Variant filter stats are: 2020-09-30 10:09:55.515 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : VARIANT_EFFECT_FILTER: pass=26921 fail=1791367 2020-09-30 10:09:55.515 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FREQUENCY_FILTER: pass=1595 fail=25326 2020-09-30 10:09:55.515 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PATHOGENICITY_FILTER: pass=1595 fail=0 2020-09-30 10:09:55.515 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : INHERITANCE_FILTER: pass=1076 fail=519 2020-09-30 10:09:55.515 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Creating analysis results from VCF /home/pchopra/tyep/vedant/SL158185/TYEP0006.SL158185.merge.filter.sorted.vcf.gz 2020-09-30 10:09:55.516 INFO 5772 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Finished analysis in 15m 40s 9ms (940009 ms) 2020-09-30 10:09:55.517 INFO 5772 --- [ main] o.m.e.c.writers.AnalysisResultsWriter : Writing results... 2020-09-30 10:09:57.712 ERROR 5772 --- [ main] o.m.e.cli.ExomiserCommandLineRunner :

htsjdk.tribble.TribbleException: Contig chr1 does not have a length field. at htsjdk.variant.vcf.VCFContigHeaderLine.getSAMSequenceRecord(VCFContigHeaderLine.java:80) at htsjdk.variant.vcf.VCFHeader.getSequenceDictionary(VCFHeader.java:206) at de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper.makeBuilder(VariantContextWriterConstructionHelper.java:97) at de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper.openVariantContextWriter(VariantContextWriterConstructionHelper.java:77) at org.monarchinitiative.exomiser.core.writers.VcfResultsWriter.writeFile(VcfResultsWriter.java:119) at org.monarchinitiative.exomiser.core.writers.AnalysisResultsWriter.writeResultsToFileForMoiWithFormat(AnalysisResultsWriter.java:83) at org.monarchinitiative.exomiser.core.writers.AnalysisResultsWriter.writeForInheritanceMode(AnalysisResultsWriter.java:77) at org.monarchinitiative.exomiser.core.writers.AnalysisResultsWriter.writeToFile(AnalysisResultsWriter.java:70) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runAnalysisAndWriteResults(ExomiserCommandLineRunner.java:129) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runAnalysisFromScript(ExomiserCommandLineRunner.java:124) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runAnalyses(ExomiserCommandLineRunner.java:83) at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.run(ExomiserCommandLineRunner.java:74) at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:813) at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:797) at org.springframework.boot.SpringApplication.run(SpringApplication.java:324) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1260) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1248) at org.monarchinitiative.exomiser.cli.Main.main(Main.java:44)

2020-09-30 10:09:57.725 INFO 5772 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-2003 - Shutdown initiated... 2020-09-30 10:09:57.734 INFO 5772 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-2003 - Shutdown completed. 2020-09-30 10:09:57.734 INFO 5772 --- [ main] org.monarchinitiative.exomiser.cli.Main : Exomising finished - Bye!`

What do I need to do/check?

thanks!

[julesjacobsen]

Is there a chr1 in the VCF header config section? Is it missing a length?

[julesjacobsen]

Closing due to lack of response.