Running SnpEff generates the following error: Fatal error: Exit code 1 (Error) Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/016/025/16025586/_galaxy_tmp -Xmx7680m -Xms256m java.lang.RuntimeException: java.io.FileNotFoundException: /cvmfs/main.galaxyproject.org/deps/snpEff/4.0/i
I am running it on a vcf pileup and selecting the genome: Bdellovibrio_bacteriovorus_HD100_uid61595
Manual download of this and selecting "reference genome from your history" stops the above error, but SnpEff download seems to have had a problem with this download and the whole of the file appears to be just the lines: Bacillus_thuringiensis_BMB171_uid49135 SnpEff4.1 So it looks like this has just downloaded the first line in a group of genomes.
Any suggestions very welcome. Thanks, Carey