Use of uninitialized value in require at (eval 792) line 1.

[GermainChev]

Hello

I got this when I run roary:

Use of uninitialized value in require at /System/Library/Perl/5.18/darwin-thread-multi-2level/Encode.pm line 60.
Use of uninitialized value in require at /System/Library/Perl/5.18/darwin-thread-multi-2level/Encode.pm line 60.
Use of uninitialized value in require at (eval 792) line 1.

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

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

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

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

And the core_gene_alignment.aln has only fasta header in it without any sequence ...

Thanks for your Help !!

Germain

[andrewjpage]

The warning is just a warning from a dependancy of a dependancy in perl. Update your perl modules.
As for not getting any core genes, that could be an installation issue, or more likely, a data issue.