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  • 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!

  • #2
    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.

    Comment


    • #3
      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~~

      Comment


      • #4
        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

        Comment

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