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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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Error with the input from Deepvariant pipeline #585

Closed genmaibutter closed 1 year ago

genmaibutter commented 1 year ago

Hi, I have error with the input form the Deepvariant pipeline.

java -Xms4g -Xmx4g -jar /data/users/test/apps/LIRICAL/LIRICAL.jar yaml -y deepvariant_LIRICAL_singleton.yml java.lang.NullPointerException at de.charite.compbio.jannovar.annotation.VCFAnnotationData.setAnnoLoc(VCFAnnotationData.java:105) at de.charite.compbio.jannovar.annotation.Annotation.toVCFAnnoString(Annotation.java:286) at de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.applyAnnotations(VariantContextAnnotator.java:398) at de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.dispatchAnnotateVariantContext(VariantContextAnnotator.java:335) at de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.annotateVariantContext(VariantContextAnnotator.java:294) at org.monarchinitiative.lirical.analysis.Vcf2GenotypeMap.vcf2genotypeMap(Vcf2GenotypeMap.java:192) at org.monarchinitiative.lirical.configuration.LiricalFactory.getGene2GenotypeMap(LiricalFactory.java:560) at org.monarchinitiative.lirical.configuration.LiricalFactory.getGene2GenotypeMap(LiricalFactory.java:547) at org.monarchinitiative.lirical.cmd.YamlCommand.runVcf(YamlCommand.java:107) at org.monarchinitiative.lirical.cmd.YamlCommand.call(YamlCommand.java:176) at org.monarchinitiative.lirical.cmd.YamlCommand.call(YamlCommand.java:33) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine.execute(CommandLine.java:2078) at org.monarchinitiative.lirical.Lirical.main(Lirical.java:39)

Do you have any recommendation for me ? Anyone have this experience before?

ielis commented 1 year ago

Hi @genmaibutter sorry for a long delay, we've been working on upgrades of the code and the docs and we just made a new release. Can you please see if the error still persists after upgrading to the latest release? Please see the revised documentation and new YAML file format.

If the problems persist, can you please share LIRICAL log and the offending variant line?

Thanks & cheers, Daniel