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'

GitHub | bioinformatician1 | 4 months ago
  1. 0

    java.lang.RuntimeException: Interval has negative coordinates

    GitHub | 4 months ago | bioinformatician1
    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'
  2. 0

    VarScan + snpEff issue

    GitHub | 3 years ago | mjafin
    java.lang.RuntimeException: Cannot read config file! Config file name : 'snpEff.config' Full path : '/ngs/oncology/analysis/external/icgc/dream/chr19_test/tumor-paired/work/snpEff.config' Config file name : '/apps/bcbio-nextgen/latest-devel/rhel6-x64/Cellar/snpeff/3.6c/libexec/snpEff.config' Full path : '/apps/bcbio-nextgen/latest-devel/rhel6-x64/Cellar/snpeff/3.6c/libexec/snpEff.config'
  3. 0

    Gene names containing spacer cause problems

    GitHub | 2 years ago | pcingola
    java.lang.RuntimeException: No white-space, semi-colons, or equals-signs are permitted in INFO field. Name:"LOF" Value:"(ILDR2 (2 of 2)|ENSDARG00000096600|1|1.00)"
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  5. 0

    Misleading error: Should be "Cannot create directory"

    GitHub | 2 years ago | pcingola
    java.lang.RuntimeException: Genome download failed!
  6. 0

    GitHub comment 47#61619854

    GitHub | 2 years ago | Kisun
    java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct.

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    Root Cause Analysis

    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.<init>()
    2. ca.mcgill.mcb
      SnpEff.main
      1. ca.mcgill.mcb.pcingola.interval.Interval.<init>(Interval.java:47)
      2. ca.mcgill.mcb.pcingola.interval.Marker.<init>(Marker.java:36)
      3. ca.mcgill.mcb.pcingola.snpEffect.HgvsDna.isDuplication(HgvsDna.java:117)
      4. ca.mcgill.mcb.pcingola.snpEffect.HgvsDna.toString(HgvsDna.java:328)
      5. ca.mcgill.mcb.pcingola.snpEffect.VariantEffect.getHgvsDna(VariantEffect.java:508)
      6. ca.mcgill.mcb.pcingola.vcf.VcfEffect.set(VcfEffect.java:1010)
      7. ca.mcgill.mcb.pcingola.vcf.VcfEffect.<init>(VcfEffect.java:260)
      8. ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.addInfo(VcfOutputFormatter.java:121)
      9. ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.toString(VcfOutputFormatter.java:297)
      10. ca.mcgill.mcb.pcingola.outputFormatter.OutputFormatter.endSection(OutputFormatter.java:111)
      11. ca.mcgill.mcb.pcingola.outputFormatter.VcfOutputFormatter.endSection(VcfOutputFormatter.java:241)
      12. ca.mcgill.mcb.pcingola.outputFormatter.OutputFormatter.printSection(OutputFormatter.java:144)
      13. ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateVcf(SnpEffCmdEff.java:354)
      14. ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:807)
      15. ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:726)
      16. ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:678)
      17. ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:773)
      18. ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:126)
      18 frames