Ragtag producing empty final file

When a fasta file displays an irregular length of sequences, ragtag crashes prematurely with error:

Wed Oct 1 17:20:27 2025 --- INFO: Reading whole genome alignments

Wed Oct 1 17:20:28 2025 --- INFO: Filtering and merging alignments

Wed Oct 1 17:20:39 2025 --- INFO: Ordering and orienting query sequences

Wed Oct 1 17:20:39 2025 --- INFO: Writing scaffolds

Wed Oct 1 17:20:39 2025 --- INFO: Writing: <path/to/workdir>/ragtag.scaffold.agp

[E::fai_build_core] Format error, unexpected "A" at line <line_number>

>example_header

TTGTAGTAGATGATGATAGTAGTAGATGATGATGA

CGTAGATGGTAAGGATAGTTAG

ATGCTAGCCCCTAGTCGATCGTGCAGCTGACTGCT <- this line causes the crash