Hello, I'm trying to use the snpEff tool lately but it has been more dificult than I thought.

build snpEff databases

mkdir /usr/local/Cellar/snpeff/4.2/share/snpeff/data mkdir /usr/local/Cellar/snpeff/4.2/share/snpeff/data/SBW25_pQBR103 cat ./ref/AM181176.embl ./ref/AM235768.embl > /usr/local/Cellar/snpeff/4.2/share/snpeff/data/SBW25_pQBR103/genes.embl

edit snpEff.config file according to documentation at the directory /usr/local/Cellar/snpeff/4.2/share/snpeff

Pseudomonas_fluorescens_with_pQBR103

SBW25_pQBR103.genome : Pseudomonas_fluorescens_with_pQBR103 SBW25_pQBR103.chromosomes : AM181176, AM235768 SBW25_pQBR103.AM181176.codonTable : Bacterial_and_Plant_Plastid SBW25_pQBR103.AM235768.codonTable : Bacterial_and_Plant_Plastid

then run the command

snpEff build -embl -v SBW25_pQBR103

And everything is fine so far. However when I'm trying to run this command: java -jar ~/bin/snpEff/snpEff.jar -no-upstream -no-downstream ./ref/SBW25_pQBR103 ./raw_vcf/SBW25_hap.vcf > ./snpEff/SBW25_hap.snpEff.vcf

I still get the error: java.lang.RuntimeException: Property: './ref/SBW25_pQBR103.genome' not found at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:106) at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:619) at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:587) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:434) at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:110) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadConfig(SnpEff.java:273) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:955) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:939) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:978) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:136)

Any thoughts what could be wrong? Do I need to create this file (SBW25_pQBR103.genome) ? Or is somehow saved somewhere? Because I couldn't find it anywhere except from the fact that it's written at the configuration file.

Thanks.