Hi @taknotts! Bummer! It looks like that perl script maybe didn't quite work as expected --- that error you posted above seems to indicate that the imported data no longer has quality scores. I feel like the manifest format shouldn't have allowed you to import quality-less sequences, so I am opening an issue to track that.
Can you provide a short snippet of one of your files, but after running the perl script on it? Something similar to what you provided in another topic would be perfect! Thanks!