MSG: Got a sequence without letters. Could not guess alphabet?

[raw937]

--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet

No idea?

[raw937]

also core genes looks funny?
Core genes (99% <= strains <= 100%) 0
Soft core genes (95% <= strains < 99%) 0
Shell genes (15% <= strains < 95%) 141
Cloud genes (0% <= strains < 15%) 9150
Total genes (0% <= strains <= 100%) 9291

[tseemann]

What was the command line and input data?

[raw937]

prokka .gff's
roary -e --mafft -p 8 *.gff -f folder_name

[andrewjpage]

There's a problem with your input dataset and it looks like you have multiple different species/genus. I would recommend you quality control your input data, for example run it through mash or kraken.