Entering edit mode
4.6 years ago
r00628112
▴
10
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
The genome file is not present.
Thanks to your reply. You mean the genome fasta file? but I already put the genome file under cd ../snpEff/data/genomes