Snpeff eff error due to missing database version

usegalaxy.org support
#1

Hi,
I’m using SnpEff-build to create a database from a Genbank file, followed by SnpEff-eff to annotate variants. The SnpEff-build tool runs without error but the database is not selectable in the SnpEff-eff tool and there is a message that says “This version of SnpEff will only work with SnpEff4.3 genome databases”. The Dataset Peek for the database shows “Snpeff version unknown” and this is the case for databases from all 4 versions of Snpeff-build. I know Snpeff-eff tool is working because I can use an earlier database (which shows “Snpeff4.3”) without issues. Is this something I can fix?

Thanks for any help

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#2

Oh, this is weird. That same combination of tools works just fine on usegalaxy.eu if that’s an acceptable workaround for you for now (just note that due to a tools bar search problem you won’t find snpeff eff there by searching for it; you will have to go to the section Variant Calling and browse all tools there to find it).

Why the same version of snpeff build behaves differently on usegalaxy.org needs to be investigated though.

#3

usegalaxy.org was switched from Python 2 to Python 3 on Tuesday, which was the source of the problem. @wm75 fixed it here and has tested it out on usegalaxy.org and it’s working again. @jole please let us know if you have any further issues with it, and thanks @wm75 for the quick fix!

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#4

Great, it’s working for me again. Thanks for the quick response!