I have been using snpff variant effect and annotation without any problems for weeks. Today I tried to carry on, but now suddenly my ref seq is not recognized (same seq I have used previously) - any ideas what may be the problem?
SnpEff genomes are built for specific versions of SnpEff. Did the version of the tool change between the different job runs (click on the rerun button of both one of your successful and failed jobs and take a look at the very top of the tool page where it says Galaxy Version x.y.z). If the versions are different, rerun your failed job with the old version (you can change the version at the very top of the tool page, too).