Question: Fail to build a database in SNPeff
0
gravatar for r00628112
11 weeks ago by
r0062811210
r0062811210 wrote:

Hi everyone:

I would like to build a database for 'Prunus mume' by following 'Option 2: Building a database from GFF files'(from the manual http://snpeff.sourceforge.net/SnpEff_manual.html)

However, I can not build a database successfully. The message is as below:

[hsiang@pomology-serverIII snpEff]$ java -jar snpEff.jar build -gff3 -v Prunus_mume
00:00:00        SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00        Command: 'build'
00:00:00        Building database for 'Prunus_mume'
00:00:00        Reading configuration file 'snpEff.config'. Genome: 'Prunus_mume'
00:00:00        Reading config file: /data/public/hsiang/tools/snpEff/snpEff.config
java.lang.RuntimeException: Property: 'Prunus_mume.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:364)
        at org.snpeff.SnpEff.run(SnpEff.java:1183)
        at org.snpeff.SnpEff.main(SnpEff.java:162)

The screen shot file is here~ https://drive.google.com/open?id=1zFyR8iOplSeq5T77nlbD1XGu1L8K1wxP

Could someone give me some suggestion for the problem?

Thank you so much

snpeff build_data_base • 94 views
ADD COMMENTlink modified 11 weeks ago by ATpoint36k • written 11 weeks ago by r0062811210
1

'Prunus_mume.genome' not found

The genome file is not present.

ADD REPLYlink written 11 weeks ago by ATpoint36k

Thanks to your reply. You mean the genome fasta file? but I already put the genome file under cd ../snpEff/data/genomes

ADD REPLYlink written 11 weeks ago by r0062811210
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