Alignment.fasta output problem, cannot make tree with FastTree

[mradz19]

I tried using Roary on the galaxy server with multiple assembled plasmid sequences (gff files from prokka annotation) using the non-paralog method, but I think I am getting strange results in my alignment.fasta output file. This is the content of the output:

15901.gff

15902.gff

15903.gff

32001.gff

32002.gff

32003.gff

32004.gff

36601.gff

36602.gff

36603.gff

36604.gff

5101.gff

5102.gff

5103.gff

5104.gff

5105.gff

7501.gff

7502.gff

7503.gff

7504.gff

7505.gff

86901.gff

86902.gff

86903.gff

When I try using that with FastTree it cannot create a tree, is that output correct for the roary alignment.fasta file? It looks like it's just a list of all the samples.