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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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MSG: Got a sequence without letters. Could not guess alphabet #586

Closed augustkx closed 1 year ago

augustkx commented 1 year ago

Dear Roary developers,

Thanks for developing such a useful tool. I met with a problem with one of the output files. I noticed that this issue has been already mentioned by several users, your advise is to make some quality control, but I have a quite normal summary_statistics.txt.

Core genes (99% <= strains <= 100%) 1120 Soft core genes (95% <= strains < 99%) 162 Shell genes (15% <= strains < 95%) 818 Cloud genes (0% <= strains < 15%) 3854 Total genes (0% <= strains <= 100%) 5954

The command is

roary -p 20 -f .log/roary -e --mafft -v ./prokka_part/*gff -g 70000 -z

I will appreciate it very much if you could give me some hints. Thanks!