Question: MAFFT 'hat2 is wrong' error
0
gravatar for wanderingstefan
22 months ago by
wanderingstefan30 wrote:

Hey all,

I am aligning merged amplicon reads (around 280-300 bp) to an initial alignment of a merged read and a reference gene for several samples using MAFFT and the --addfragments option. It works just fine for the great majority of samples (20/24), but for some I get the very uninformative error 'hat2 is wrong', resulting in an empty output file. I am aware of Mafft Output Distance Matrix and https://www.biostars.org/p/184512/, but these do not really provide information about the error. The command I run is

mafft --addfragments read_file --keeplength --reorder --thread 40 alignment_in > alignment_out

and the error: Loading 'hat2n' (aligned sequences - new sequences) ... 109626 != 10962 hat2 is wrong

Since hat2 seems to encode a distance matrix and the sequence numbers match except for the last number, is it possible that the matrix is somehow truncated? The strange thing is that I do not get the error with reads from the same sample when I map them to another reference gene. Other samples however work with that reference gene but not with the other.

Does somebody have a clue what is going on here?

Cheers

ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 22 months ago by wanderingstefan30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1975 users visited in the last hour