Hello! I am building an annotation database according to the manual of SnpEff. I got the error warning as following:
Blockquote
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
Blockquote
Does someone know how to fix it? Thank you very much
Can you specify the command you have used for building the db? For other hand, have you edited the
snpEff.config
file? You need to add an entry with for the genome you want to build a database:IRGSP1.genome
, in your case.