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Old 12-17-2014, 05:12 PM   #1
maryb
Junior Member
 
Location: CA

Join Date: Jan 2012
Posts: 6
Default error generating database in snpEFF

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!
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Old 12-17-2014, 11:14 PM   #2
wolma
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Location: Germany

Join Date: May 2014
Posts: 23
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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.
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Old 03-06-2016, 05:38 PM   #3
wyll
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Location: TW

Join Date: Feb 2016
Posts: 6
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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~~
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Old 03-06-2016, 05:45 PM   #4
GenoMax
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Location: East Coast USA

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Posts: 6,966
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Quote:
Originally Posted by wyll View Post
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
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