error generating database in snpEFF

[maryb]

hi all,
I am trying to use snpEff (http://snpeff.sourceforge.net/).



when i try to build my genomedatabse, I keep getting the same error message as "java.lang.RuntimeException: Property:
'/Volumes/Seagate_Exp_1/snpEff/data/AsinC2.1.genome' not found".


Also when i use "java -jar snpEff.jar" i get the error message "Error: Unable to access jarfile snpEff.jar".

I have the following locations for java and snpEff:

JAVA:

/usr/bin/java

java -version
java version "1.8.0_25"
Java(TM) SE Runtime Environment (build 1.8.0_25-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.25-b02, mixed mode)

***************
snpEff:

/usr/local/bin/snpEff


any idea of where my mistake is? any suggestion would be greatly appreciated!

[wolma]

Hi,
you need to run your "java -jar snpEff.jar" command from *inside* the folder that has your snpEff installation (in your case do a: cd /usr/local/bin/snpEff).

Seeing that you installed your snpEff into /usr/local/bin, I assume you wanted to make sure it's in your path. Problem is: you do not run it as a stand-alone command. In java -jar snpEff.jar the command is java, the rest are just options, so your shell uses $PATH to locate java, but that's all path resolution is used for here. In other words, it doesn't make much sense to put snpEff into a system bin folder.

[wyll]

I have a question about the reference database.

Following the command given on the SnpEff manual,
java -jar snpEff.jar download -v hg19
I got the hg19 in the form of a bunch of .bin files.

Don't really know how to use them, any suggestions?

Thank you~~

[GenoMax]

I have a question about the reference database.

Following the command given on the SnpEff manual,
java -jar snpEff.jar download -v hg19
I got the hg19 in the form of a bunch of .bin files.

Don't really know how to use them, any suggestions?

Thank you~~

Did you see the help pages on how to run SnpEff: http://snpeff.sourceforge.net/SnpEff_manual.html#run