MAFFT freezes and nothing happens for over 2 hours

Question

[langziv]

Hi.
I'm using MAFFT for multiple sequence alignment for 7 closely related bacterial genomes (the resulting file will be used for creation of a phylogenetic tree).
I used the following command:

mafft --thread -1 --auto all_genomes.fna > output.fna

The input file is a FASTA file with genomes of various strains of a bacteria genus. The output file remains empty.
When the run starts the program prints the following text:

OS = linux
The number of physical cores =  4
reallocating...
done.
nthread = 4
nthreadpair = 4
nthreadtb = 4
ppenalty_ex = 0
reallocating...
done.
stacksize: 8192 kb
reallocating...
done.
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

There are 289 ambiguous characters.
    1 / 7 (thread    0)
done.

Constructing a UPGMA tree (efffree=0) ...
    0 / 7
done.

Progressive alignment 1/2...

len1=4928223, len2=4350020, Switching to the memsave mode
STEP     4 / 6 (thread    3)mDP 00001 / 00647

Do you have an idea how to solve this?
Thanks.

[andres.firrincieli]

You can't use MAFFT for the alignment of whole genomes

[langziv]

Thanks.
Do you know a program that's suited for whole bacterial genome?
I see that it's not trivial to do such an alignment. I got 7 genomes for which I need to do multiple sequence alignment together, in order to create a phylogenetic tree.

Answer 1

[andres.firrincieli]

for phylogenomic analysis of microbial strains you can use GToTree

edit: or follow the Anvi'o worflow for phylogenomics: link