I ran roary on galaxy europe for 37 e coli genomes but the core genome alignment file output is empty, there is no sequences in there.
Duplicated post, see Roary troubleshooting (version 3.13.0+galaxy2 or later)
If you would like more help, please post back a shared history link to the original topic.
Before you do that, please try at least one more rerun. The UseGalaxy.eu server had some technical issues earlier this week that may have contributed to failures.