Question: error in building annotation database by SnpEff
0
gravatar for lifengmail
3.2 years ago by
lifengmail10
lifengmail10 wrote:

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

software error • 1.6k views
ADD COMMENTlink written 3.2 years ago by lifengmail10

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.

ADD REPLYlink written 3.2 years ago by iraun3.5k
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