Welcome @sche2021
The tool should work fine with a dataset collection input but it might have trouble with very large inputs or very large genomes or possibly input reads that haven’t gone through upstream quality assurance steps.
We have tutorials here to demonstrate usage with the tool if you want to compare→ GTN Tutorials for Flye: de novo assembler for single molecule sequencing reads
And if you would like us to help more, I’m curious about your exact error, what the data looks like, and which server you are working at (since server resources could be another factor!). If you want to share your history we can help to review these details and make suggestions. See the banner at this forum or here How to get faster help with your question 