[maker-devel] Running MAKER on highly fragmented assembly

[Daniel Ence]

Hi Mikael, Depending on the genome size, the assembly you've described shouldn't be too difficult to work with. The process activity that you're describing sounds more like a race condition, where one process is hogging all the work and all the other processes keep trying to find work, but keep getting in each others' way. 

How much of the genome has maker completed when the processes start doing this?

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Mikael Brandström Durling [mikael.durling at slu.se]
Sent: Wednesday, February 20, 2013 6:12 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] Running MAKER on highly fragmented assembly

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
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