Welcome, @BenMulder
It is difficult to know for certain but it seems possible that the server where you are working couldn’t handle a larger processing job if you are inputting over 5k nucleotide sequences for a six-frame translation job!
As a potential work-around, you could split the larger file up into smaller files, process each of those, then merge the results back together. Whether this is appropriate depends on the tool but the one you are using is probably Ok for this.
The process usually goes something like this. It runs in a batch, and if you put all of the tools into a simple workflow, it would run almost like a single (custom) tool.
If this helps, please let us know. If you still need more help, please share more details. For what you explain, the server where you are working and the exact tool name/version are likely the most important details.
- Troubleshooting resources for errors or unexpected results
- How to get faster help with your question
Let’s start there, thanks! 