Question: SnpEff Custom DB for Recombinant virus
0
gravatar for skbrimer
3.1 years ago by
skbrimer640
United States
skbrimer640 wrote:

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

snp genome • 2.2k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by skbrimer640
1

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

ADD REPLYlink written 3.1 years ago by skbrimer640
2
gravatar for Pierre Lindenbaum
3.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

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

ADD COMMENTlink written 3.1 years ago by Pierre Lindenbaum131k

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.

ADD REPLYlink written 3.1 years ago by skbrimer640

can you please validate my answer please.

ADD REPLYlink written 3.1 years ago by Pierre Lindenbaum131k
1

Sure will! Thank you for the help!

ADD REPLYlink written 3.1 years ago by skbrimer640
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