snpEff get latest version of java and doesn't work.

bioconda / bioconda-recipes

Conda recipes for the bioconda channel.

https://bioconda.github.io

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snpEff get latest version of java and doesn't work. #14323

Open Slugger70 opened 5 years ago

Slugger70 commented 5 years ago

New installs of snpEff are getting java version 11 and snpEff requires java version 8.

When you run snpEff with java 11 it runs to completion but doesn't output anything, no error messages either.. :( But when it's run with version 8 it all works fine.

When I downgraded the version of java installed in snpEff env to openjdk=8.0.192 everything worked as expected.

cbrueffer commented 5 years ago

Do you use the -t flag (multithreading) by any chance? Things work here with JDK 11 and the defaults (no multithreading), but I see the problem you describe with -t.