Sequences Missing in core_gene_alignment.aln file

[fphage]

Installed ROARY on Biolinux 8 Roary installation checked using roary -a Everything is looking fine I ran the following command roary -e -n --mafft -p 8 -t 1 -r -f foldername .*gff

After analysis There are no aligned sequences in the core_gene_alignment.aln file - It contains only the headers

Any help

Thanks

[tseemann]

@fphage you'll leed to provide the output log file. maybe run it again with roary -v YOUR_STUFF 2>&1 > roary.log

[andrewjpage]

I noticed that you change the translation table to. 1. What type of bacteria is it?

On 5 Sep 2017 4:41 pm, "fphage" notifications@github.com wrote:

Installed ROARY on Biolinux 8 Roary installation checked using roary -a Everything is looking fine

I ran the following command roary -e -n --mafft -p 8 -t 1 -r -f foldername

After analysis There are sequences in the core_gene_alignment.aln file - It has only the headers

Any help

Thanks

.

[fphage]

@andrewjpage

My files belong to bacteriophages. In the ROARY user manual suggested translation table is 1 for viruses

[yanadya]

Bacteriophages are quite diverse - I will not be surprised if there are no core in your collection. Try to lower % of similarity.

[fphage]

@tseemann summary_statistics.txt Log file attached

[fphage]

roary.log.txt Logfile

[fphage]

@yanadya I will try using lower % The phage genomes i was using as input are highly identical.