Unix fold command behaving strangely

So I have this fasta (biology) file that looks like this: >m64093_191209_130050/133911/ccs_64 TTCAGGCTGTGTTCCATTTGATTTAAAATCAAATAATTTCATTCGCGTCAGAACACCTGGTTTCACGACC ATAAATAATTTACCAGTGAATCGAGGCTCAATTATAGATCCTCGGACGCGAGTTCTCGGTTGACGAGTGG GATTCGAATTATTTTTCACCGAAAATTTTAGTCGACGAGTTCAGATAAATTTGTTCGGGATAAAATCATC TGAGTAGGTCGGGCTTCTGAATTTCGTATTCTTGCGAGCAATGAATTTTAAATAATCATCGGACATACCA ATTTTTGGAACAATAATGTTCCGAACATCCCGAAAATATAGGAAGAGCCCGGATAGATAAAAATAAACAC Each line is max 70 chars long. Usually, if I want to format it to max 50 characters long, I use: > fold -50 input.fasta > output.fasta # also tried -b and -w args But somehow this is not working. The file looks exactly the same as many others I've seen. The output now looks like this: >m64093_191209_130050/133911/ccs_64 TTCAGGCTGTGTTCCATTTGATTTAAAATCAAATAATTTCATTCGCGTCA GAACACCTGGTTTCACGACC ATAAATAATTTACCAGTGAATCGAGGCTCAATTATAGATCCTCGGACGCG AGTTCTCGGTTGACGAGTGG GATTCGAATTATTTTTCACCGAAAATTTTAGTCGACGAGTTCAGATAAAT TTGTTCGGGATAAAATCATC TGAGTAGGTCGGGCTTCTGAATTTCGTATTCTTGCGAGCAATGAATTTTA AATAATCATCGGACATACCA ATTTTTGGAACAATAATGTTCCGAACATCCCGAAAATATAGGAAGAGCCC It cuts overhanging 20 characters and correctly places them bellow, but then it's not joining the next line and cutting it on max 50 chars as it should. I went back to previous fasta files I created and the fold command still works normally. The problem persists if I copy a segment of the new file and past it in another file. I think there might be an encoding problem that I'm not aware of. Can anyone help? Cheers, EDIT: Great answers, thanks!!