[maker-devel] altest without MPI?

[Jacqueline R M Doyle]

Hi!

I am beginning my first MAKER annotation and had a quick question.  I am currently planning on following the “Training ab initio Gene Predictors” section of the MAKER 2012 tutorial.  For my species of interest, I have 784290 scaffolds in which 80% are greater than 100 kb.  I have EST data from a closely related species and was also going to use the core cegma protein sequences.  With this in mind, I made the following changes to my maker_opts file:

genome=scaffolds.fasta
altest=Trinity.fasta
protein=cegma.fa
est2genome=1
cpus=48

My primary concern is that this is going to take a long time to run with altest, even with the extra cpus for BLAST.  The software was not originally installed on our computer cluster with MPICH2, but I may be able to talk our computer guys into reinstalling if the situation is going to be completely untenable without MPI.  I guess my question is, is there any point in trying to run the above without MPI?  Is there a good way to monitor the progress of such a run if I was to give it a shot?   

Thanks for your help with this!

Jackie