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'

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Solutions on the web

via GitHub by bioinformatician1
, 1 year ago
Interval has negative coordinates. Class : Marker Start : -15 End : 4 ID : Parent class : Chromosome Parent : scaffold_148 0-411 CHROMOSOME 'scaffold_148'
via GitHub by chapmanb
, 1 year ago
Interval error: end before start. Class : Marker Start : 0 End : -1 ID : Parent class : Chromosome Parent : GL000241.1 0-42151 CHROMOSOME 'GL000241.1'
via GitHub by bwubb
, 1 year ago
Interval error: end before start. Class : Marker Start : 0 End : -1 ID : Parent class : Chromosome Parent : GL000241.1 0-42151 CHROMOSOME 'GL000241.1'
via GitHub by bwubb
, 1 year ago
Interval error: end before start. Class : Marker Start : 0 End : -1 ID : Parent class : Chromosome Parent : GL000220.1 0-161801 CHROMOSOME 'GL000220.1'
via GitHub by trutane
, 1 year ago
Interval error: end before start. Class : Marker Start : 879960 End : 861120 ID : Parent class : Chromosome Parent : 1 0-249250620 CHROMOSOME '1'
via GitHub by amphun
, 1 year ago
Interval error: end before start. Class : Marker Start : 19948 End : 19161 ID : Parent class : Chromosome Parent : 1 0-8033584 CHROMOSOME '1'
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.(Interval.java:47)
at ca.mcgill.mcb.pcingola.interval.Marker.(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.(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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