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snpEff.config Error

Hello guys I have a problem with the snpEff. config. I have an apricot gff3 file I converted it to gtf file and then I have a reference apricot fasta file. to build snpEff.config I used the command below step by step

Firstly, I create a new directory for my genome in the snpEff data folder mkdir myGenome folder

And then I moved he GTF and FASTA files to the myGenome directory

after that, I used the command:

vi snpEff.config 
myGenome.genome: Apricot

and then I wrote the command below to build

snpEff build -gtf22 -v myGenome

But I got an Error. Could you pls help me with the issue?

this is the Error

snpEff build -gtf22 -v myGenome                        
00:00:00 SnpEff version SnpEff 5.1 (build 2022-01-21 06:23), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'myGenome'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'myGenome'
00:00:00 Reading config file: /Users/uguremre/snpEff/snpEff.config
java.lang.RuntimeException: Property: 'myGenome.genome' not found
    at org.snpeff.interval.Genome.<init>(Genome.java:104)
    at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:784)
    at org.snpeff.snpEffect.Config.readConfig(Config.java:751)
    at org.snpeff.snpEffect.Config.init(Config.java:529)
    at org.snpeff.snpEffect.Config.<init>(Config.java:116)
    at org.snpeff.SnpEff.loadConfig(SnpEff.java:429)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:399)
    at org.snpeff.SnpEff.run(SnpEff.java:1141)
    at org.snpeff.SnpEff.main(SnpEff.java:160)
00:00:00 Logging
00:00:02 Done.
snpeff config
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written by bestone • bestone

1 answer

And then I moved he GTF and FASTA files to the myGenome directory

that's not enough. the config file must be edited https://pcingola.github.io/SnpEff/se_build_db/#add-a-genome-to-the-configuration-file

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

I tried all the steps in the link you shared. But I couldn't find where I made a mistake

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written by bestone • bestone

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