mafft - The-Bioinformatics-Group/Albiorix GitHub Wiki

Commands(s):

• mafft
• linsi
• einsi
• ginsi

Installed in:

/usr/local/bin

Notes:

Mafft will print information on the alignment process to STDERR and the resulting alignment to STDOUT. This causes problems when running an analysis on one of the compute nodes AND using the queue system (e.g. using qlogin etc.), since the necessary permissions to "/dev/stderr" is not set correctly by SGE. A solution to this problem is to redirect STDERR to a separate file (e.g. add "2> err.txt" to your command), or to use the "--quiet" option with mafft like this:

• mafft --quiet seq.fst > out.fst

or

• mafft seq.fst 2> err.txt 1> alignment.fst