Abnormal reading of FASTA file by PAL2NAL

[atape]

I am making a script that produces as an output a protein alignment in fasta format and an appropriate mRNA fasta file for latter use with the PAL2NAL algorithm that gives a codon aware alignment.

PAL2NAL is reading the mRNA fasta file normally, the same cannot be said for the protein file. This is the error that the web based interface gives:

ERROR: number of input seqs differ (aa: 82; nuc: 43)!!

It is reading the fasta file as if it has 82 sequences, when it really has the same amount as the mRNA fasta file. I've never had this problem before, what am I missing? Thank you for the help . Attached are both files.

https://www.dropbox.com/s/z9k0pkr5g1...fFT.fasta?dl=0 Protein alignment

https://www.dropbox.com/s/jpgdz213oa...FFT.fasta?dl=0 mRNA file