SnpEff Custom DB for Recombinant virus

Question

[skbrimer]

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.

Sean

[skbrimer]

The short answer is make sure you do all the steps in the documentation. Boy do I feel silly.

Answer 1

[Pierre Lindenbaum]

where did you put the FW200_Anno.gb file relative to the snpEff/data/ dir ? how did you edit the snpeff config file ? http://snpeff.sourceforge.net/SnpEff_manual.html#databases

[skbrimer]

You are correct, I forgot to edit the snpeff.config file. I had the files in the data dir just forgot to do step two.

[Pierre Lindenbaum]

can you please validate my answer please.

[skbrimer]

Sure will! Thank you for the help!