Good Morning Hive mind,
I am using SnpEff v4 to attemp to make a custom database of a recombinant virus we made in house. I have annotated the genome using DNAStar SeqNinja which uses Mauve to map genes from a reference to your genome and then outputs a genbank file.
So I have my file, FW200_Anno.gb and I'm following the SnpEff documentation to add a custom database to it's data set. With the basic command:
java -jar snpeff.jar -v build -genbank FW200_Anno.gb
I am in the snpeff directory like it says but I get the following output and error
00:00:00 SnpEff version SnpEff 4.3r (build 2017-09-06 16:41), by Pablo Cingolani 00:00:00 Command: 'build' 00:00:00 Building database for '/home/sbrimer/Desktop/FW200_Anno.gb' 00:00:00 Reading configuration file 'snpEff.config'. Genome: '/home/sbrimer/Desktop/FW200_Anno.gb' 00:00:00 Reading config file: /home/sbrimer/software/snpEff/snpEff.config java.lang.RuntimeException: Property: '/home/sbrimer/Desktop/FW200_Anno.gb.genome' not found at org.snpeff.interval.Genome.<init>(Genome.java:106) at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681) at org.snpeff.snpEffect.Config.readConfig(Config.java:649) at org.snpeff.snpEffect.Config.init(Config.java:480) at org.snpeff.snpEffect.Config.<init>(Config.java:117) at org.snpeff.SnpEff.loadConfig(SnpEff.java:451) at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:363) at org.snpeff.SnpEff.run(SnpEff.java:1183) at org.snpeff.SnpEff.main(SnpEff.java:162) 00:00:00 Logging 00:00:01 Done.
It says it can not find
FW200_Anno.gb.genome which is fair there is no such file but I don't understand this error at all. Has anyone run into this error before?
Any help is appreciated and thank you in advance.