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  • fc35802
    replied
    I am not authorized to download to our server, so I have to ask someone to install all the programs.

    So I use the command exactly as it is, but with -c and the path to snpEff.config ?

    Leave a comment:


  • mehc
    replied
    Anything's possible in a possible world

    If I remember correctly, with the default install, it should be in the same directory

    Leave a comment:


  • fc35802
    replied
    I have snpEff in one place and snpEff.config in another.

    That is possible?

    Leave a comment:


  • mehc
    replied
    Do you have snpEff.config in /GenoStorage/Software/snpEff_2_0_5d/ ?

    If it's elsewhere you can specify that with -c

    Leave a comment:


  • fc35802
    started a topic snpEff error

    snpEff error

    Can you see the error in here?

    Thanks in advance




    java -Xmx4G -jar /GenoStorage/Software/snpEff_2_0_5d/snpEff.jar eff -v -onlyCoding true -i vcf -o txt /GenoStorage/BasesDados/GRCh37.64 varSample02187ATESTE.flt.vcf > snpEff_sample02187A.vcf
    00:00:00.000 Reading configuration file 'snpEff.config'
    java.lang.RuntimeException: Cannot find config file 'snpEff.config'
    at ca.mcgill.mcb.pcingola.snpEffect.Config.read(Config.java:117)
    at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:46)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:523)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:244)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:72)
    00:00:00.007 Finishing up

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