The output file generated by galaxy in core gene alignment is empty. I’ve tried everything, I changed Galaxy to Australia and galaxy.com and I’m having the same problems. I ran an analysis in September and it was successful, and now this problem has repeated itself for 10 attempts. I tried to modify the file names, I ran prokka more than once. I’ve seen that this problem has occurred with other users but I haven’t been able to resolve it through the instructions given to these people.ro In fact, the other files come out normal, the core gene alignment comes out empty. I used 43 genome. In the last analysis I did I used more than 100 and got positive results. Anyway, thank you.
Someone else recently posted about this here: Problems with roary output
And prior help is in here: roary core genome alignment file is empty. (resolved) - #7 by jennaj
So, one of these is going on:
- the job is “too large” for the public servers
- the input files are not named in a way that Roary can use
If you want to share your example we can try to help more.