MAFFT freezes and nothing happens for over 2 hours
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.
1 answer
for phylogenomic analysis of microbial strains you can use GToTree
edit: or follow the Anvi'o worflow for phylogenomics: link
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You can't use MAFFT for the alignment of whole genomes
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.