java.lang.RuntimeException

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  • VarScan + snpEff issue
    via GitHub by mjafin
    ,
  • GitHub comment 47#61619854
    via GitHub by Kisun
    ,
  • GitHub comment 11#40010038
    via GitHub by pcingola
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  • GitHub comment 3895#149587934
    via GitHub by fdlk
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  • GitHub comment 1205#189271404
    via GitHub by bwubb
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    • java.lang.RuntimeException: Interval has negative coordinates. Class : Marker Start : -15 End : 4 ID : Parent class : Chromosome Parent : scaffold_148 0-411 CHROMOSOME 'scaffold_148' at ca.mcgill.mcb.pcingola.interval.Interval.<init>(Interval.java:47) at ca.mcgill.mcb.pcingola.interval.Marker.<init>(Marker.java:36) at ca.mcgill.mcb.pcingola.snpEffect.HgvsDna.isDuplication(HgvsDna.java:117) at ca.mcgill.mcb.pcingola.snpEffect.HgvsDna.toString(HgvsDna.java:328) at ca.mcgill.mcb.pcingola.snpEffect.VariantEffect.getHgvsDna(VariantEffect.java:508) at ca.mcgill.mcb.pcingola.vcf.VcfEffect.set(VcfEffect.java:1010) at ca.mcgill.mcb.pcingola.vcf.VcfEffect.<init>(VcfEffect.java:260) at ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.addInfo(VcfOutputFormatter.java:121) at ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.toString(VcfOutputFormatter.java:297) at ca.mcgill.mcb.pcingola.outputFormatter.OutputFormatter.endSection(OutputFormatter.java:111) at ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.endSection(VcfOutputFormatter.java:241) at ca.mcgill.mcb.pcingola.outputFormatter.OutputFormatter.printSection(OutputFormatter.java:144) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateVcf(SnpEffCmdEff.java:354) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:807) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:726) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:678) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:773) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:126)
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