I have used mafft to align multifasta files with a txt extension. I made the attached work flow, trying to get one file per multifasta file, that contains the consensus sequence in fasta format for downstream analysis. I am getting an error that my input files are not in the correct format. They look something like this:
>TAGCTAGCTAGC
--TAGCTAGC--TAGC-T-TAGC----GGG
>TAGCTAGCTAGC
AGTAGCTAGCCTAGC---TAGCCT-GG-

How can I use these .txt files in fasta format, previously aligned using mafft, and UGENE to produce one file per multifasta file with a consensus sequence, such as the following (depending on the parameters used to generate consensus sequence)
>TAGCTAGCTAGC
--TAGCTAGC--TAGC---TAGC----GG

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I tried to do the same workflow and test it.

I can't reproduce issue you described.

Your workflow looks correct, it can produce an error only if the input folder contains some files that are not in fasta or any other msa format.

Could you please send us the workflow and input data you used?

You can send it to ugene@unipro.ru