No word from the helpful Gibbs expert who offered to test my file with the new 'centroid' motif-finding software to find out why it ran so much slower than the previous version. I suspect he wasn't able to find a solution.
So today I'm going to collect the genome sequences from the other Pasteurellaceae and queue up searches using the old Gibbs motif sampler. I'll specify to the queueing program (on the shared computer cluster) that they might take 2 days, and make sure to ask for enough memory, so that the runs aren't terminated by the system before the Gibbs program has completed searching and analyzing the results. Because the Gibbs program is stochastic, I'd better do the runs at least in duplicate.
19 hours ago in Variety of Life