I was wondering if any of you has an idea of a way by which I can profile my runs. What I mean is I'd like to know how much time was spent on each step of the analysis - am I spending most of the time masking repeats, blasting transcripts/proteins, running ab-initio predictors etc. Based on this information, I might want to adjust my configuration, e.g. maybe I'm spending a lot of time blasting transcripts, and reducing the number of input transcripts would reduce run time significantly without having a major effect on results quality.
As far as I can see, the main run log does not provide such information, and I'm not sure where else to look. Any ideas or directions could be of help.