Please cite Roary if you use any of the results it produces:
    Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,
	"Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693
    doi: http://doi.org/10.1093/bioinformatics/btv421
	Pubmed: 26198102

Extracting proteins from /home/manager/pangenome_roary/Roary3/Funu1_annotated.gbk.gff
Extracting proteins from fixed_input_files/Funu2_annotated.gbk.gff
Extracting proteins from fixed_input_files/S10A_Node1.gbk.gff
Extracting proteins from fixed_input_files/S10D_Node145.gbk.gff
Extracting proteins from fixed_input_files/S10D_Node78.gbk.gff
Extracting proteins from fixed_input_files/S21A_Node4.gbk.gff
Extracting proteins from fixed_input_files/S45V1_LOC_1.gbk.gff
Extracting proteins from fixed_input_files/S45V1_Node1.gbk.gff
Extracting proteins from fixed_input_files/S45V2_Node4.gbk.gff
Extracting proteins from fixed_input_files/S45V3_Node19.gbk.gff
Extracting proteins from fixed_input_files/S45V4_Node1.gbk.gff
Extracting proteins from fixed_input_files/S68-1_Node1.gbk.gff
Extracting proteins from fixed_input_files/S68-2_Node1.gbk.gff
Combine proteins into a single file
Iteratively run cd-hit
Parallel all against all blast
Cluster with MCL
Aligning each cluster