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  • error in building annotation database by SnpEff

    Hello!
    I am building an annotation database according to the manual of SnpEff.
    I got the error warning as following:
    00:00:00 SnpEff version SnpEff 4.2 (build 2015-12-05), by Pablo Cingolani
    00:00:00 Command: 'build'
    00:00:00 Building database for 'IRGSP1'
    00:00:00 Reading configuration file 'snpEff.config'. Genome: 'IRGSP1'
    00:00:00 Reading config file: /.../snpEff/snpEff.config
    java.lang.RuntimeException: Property: 'IRGSP1.genome' not found
    at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:106)
    at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:619)
    at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:587)
    at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:434)
    at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:110)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadConfig(SnpEff.java:273)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:340)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:978)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:136)
    00:00:00 Logging
    Does someone know how to fix it?
    Thank you very much

  • #2
    Hi loyaltman,
    I encountered the same exact error this week actually. It looked like a bug within the new update to me. I switched to a previous version (4.1g (build 2015-05-17). It worked like a charm! So, I would just try downloading this version and see if it works for you.
    Cheers!

    Comment


    • #3
      hello, burgerjohnjohn.
      Thank you very much, I will try.

      Comment

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