Question: snpEff installation, unable to download reference genome
gravatar for swethabiochem
9 months ago by
swethabiochem0 wrote:

Hello All, I am trying to install snpEff installation and getting the following errors could you help me regarding this.



./snpEff.config: line 17: data.dir: command not found
./snpEff.config: line 22: database.repository: command not found
./snpEff.config: line 27: versions.url: command not found
./snpEff.config: line 35: database.clinvar.GRCh38: command not found
./snpEff.config: line 36: database.repository.clinvar: command not found
./snpEff.config: line 38: database.dbsnp.GRCh38: command not found


java -jar snpEff.jar download GRCh38.76

java.lang.RuntimeException: Property: 'GRCh38.76.genome' not found
    at org.snpeff.interval.Genome.<init>(
    at org.snpeff.snpEffect.Config.readGenomeConfig(
    at org.snpeff.snpEffect.Config.readConfig(
    at org.snpeff.snpEffect.Config.init(
    at org.snpeff.snpEffect.Config.<init>(
    at org.snpeff.SnpEff.loadConfig(
    at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(
    at org.snpeff.SnpEff.main(
snp • 608 views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 9 months ago by swethabiochem0

I think that your command should be:

java -Xmx4g -jar snpEff.jar download -c snpEff/snpEff.config -v GRCh38.76


ADD REPLYlink written 9 months ago by Kevin Blighe60k

The snpEff.config file is not an executable file. Did you follow these guidelines closely?

Is your /data/ directory properly set within the snpEff.config file?

ADD REPLYlink written 9 months ago by Macspider3.0k
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