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

[allebiotech]

Hi, I've run Roary on 17 closely related strains but when I try to run the Roary script (pan_genome_core_alignment) to include an outgroup into the core alignment, a warning comes out:

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

I've tried to add this: -alphabet=>'dna' in the MergeMultifastaAlignments.pm but nothing changed (maybe I did it wrong? I'm not an expert user).

This issue was labelled as "bug" in 2016. Are there any new feedback?

My summary statistics file says:

Core genes (99% <= strains <= 100%) 1759
Soft core genes (95% <= strains < 99%) 0
Shell genes (15% <= strains < 95%) 2106
Cloud genes (0% <= strains < 15%) 3282
Total genes (0% <= strains <= 100%) 7147

Thanks in advance!

[andrewjpage]

Hi, You need to include the outgroup along with the other files when you run roary. Andrew

…

On Wed, 25 Jul 2018, 14:34 allebiotech, ***@***.***> wrote: Hi, I've run Roary on 17 closely related strains but when I try to run the Roary script (pan_genome_core_alignment) to include an outgroup into the core alignment, a warning comes out: MSG: Got a sequence without letters. Could not guess alphabet . I've tried to add this: -alphabet=>'dna' in the MergeMultifastaAlignments.pm but nothing changed (maybe I did it wrong? I'm not an expert user). This issue was labelled as "bug" in 2016. Are there any new feedback? My summary statistics file says: Core genes (99% <= strains <= 100%) 1759 Soft core genes (95% <= strains < 99%) 0 Shell genes (15% <= strains < 95%) 2106 Cloud genes (0% <= strains < 15%) 3282 Total genes (0% <= strains <= 100%) 7147 Thanks in advance! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#410>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeV1TrH3UBv_Gcu-9Z8cl_tAA_PIO_ks5uKHPpgaJpZM4VgGAF> .

[Guanguan8]

-------------------- WARNING ---------------------
MSG: Seq [GKOOBEJB_00026]: Terminator codon inside CDS!
--------------------- WARNING ---------------------
MSG: Seq [GKOOBEJB_00027]: Terminator codon inside CDS!
This happens when I annotate genomes by prokka, and I try to run the Roary script ，a same warning comes out:

MSG: Got a sequence without letters. Could not guess alphabet .
Are there any new feedback?

[allebiotech]

Thanks a lot @andrewjpage, it works! 👍

[andrewjpage]

@Guanguan8 Its an issue with Prokka: tseemann/prokka#203

[Guanguan8]

@andrewjpage，
But I'm looking at Mycoplasma's which may use a different translation table，How to solve it？
Thanks in advance!