[maker-devel] Running MAKER on highly fragmented assembly

[Mikael Brandström Durling]

Hi,

I'm trying to run MAKER on a rather fragmented assembly. I know this is not optimal, as I will most likely miss a substantial part of the gene complement due to the fragmentation. Disregarding this, my question is if there are other problems with running maker on these kinds of genomes with roughly 1500 scaffolds and an N50 of 60 kb? I find that maker, run with MPI (mpich2) behaves rather in a rather strange way, with basically one of the ranks staying at 100% cpu, and the others lingering at about 0%. Now and then I see a burst of activity in the other ranks before they get back to low activity. Could this be a result of the fragmentation level, or should I look for other problems? (Like the all to common problems of running over NFS with locking etc).

cheers,
Mikael