MLST sequences are shorter than their reference

[MostafaYA]

Hey,
Thanks for developing ariba,
I am using ariba for MLST calling. My scheme is not available online so I've created a custom scheme (issue #185 ). I am interested to get the sequences of each locus from all strains for further alignment and phylogeny.
These sequences should be in the file (assembled_seqs.fa).
My issue is:
Some of the sequences are shorter than the reference (2-6 nucleotide short). Also the file (assembled_genes.fa) in all of my strains is empty.
I used the option '--gene_nt_extend' at 1000 but no improvement.
I would appreciate telling how I can fix that to get the full lengths as in reference

Thanks a lot,
MA

[andrewjpage]

Its impossible to say really without seeing the file you are working with. I would make sure the are no frameshifts in the sequences.