get.oturep 'crashes' mothur


I have the following problem:

mothur > get.oturep(,,, label=0.03)

Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
[19:09:21][till@kw2091: mothur]$

The ‘killed’ comes up after the matrix reading progress bar has been full for 1 or 2 minutes. I’m not even sure if the ‘Killed’ output comes from mothur or the OS. It happens every time I try it, at least with these files (I don’t have different ones to try at the moment). Any ideas what may cause this? I run mothur on an 8 core workstation with 24 GB RAM and Fedora.



You could try setting large=T. Then mothur will not store the distance matrix in RAM.