Let’s combine your two questions. Xref → File size limit exceeded during align.seqs
You are working at UseGalaxy.org, correct? And the reference data worked for you before at this same server or a different server?
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If this exact same database worked with different data, and you are working at UseGalaxy.org, then the job is likely exceeding computational resources at the server due to some difference in the query. That could be size but also read composition factors. You could try at a server that can scale a bit larger – UseGalaxy.eu is a good choice.
Transferring data between servers can be done by URL, individual files or an entire history (consider simplifying that history first for faster compression and transfer: copy the important files into a new simple history, then transfer that).
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If you are working somewhere else, I would still try at Galaxy.eu to see what happens. You could at least learn if the target database is the problem, or if it is the query.
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If you think that the reference has a problem, do you want to share where you sourced it for feedback? You could also share what that data looks like in a history with a small testing sort of query to get the bug report with error details captured. How to share your work is in the banner at this forum, also here → How to get faster help with your question. I’ll try to help but we can also bring in other scientists in our community who work with this data more often – they’ll appreciate the context (chat link).
Meanwhile, I am going to look up the current resource allocation for Align.seqs at these two servers to confirm/compare that everything is as expected.
Hope this helps and please let us know how this works out or if you need more help! 