Some confusions about optimize_augustus.pl
Posted: Mon Nov 30, 2015 2:51 am
Hi guys,
I am using optimize_augustus.pl to optimize my 'new' species. But It has been taking over six days on 24 CPU =-= importantly, the time will be out soon because I set the max running time is 6 days and 23 hours. So I have two confusions here, could you help me figure out^^?
my command line looks like:perl optimize_augustus.pl --species=As As.genes.gb.train
1. I did not set the option --cpus=24, so if I would not set the cpus number, dose the script only use 1 cpu?
2. As I describe above, The time will be out soon and the optimize_augustus.pl won't be finished, so, do any commands or scripts could continue the unfinished optimize training? And also, I found the cue (After optimize_augustus.pl has finished or (after you have interrupted it) you should (re)train AUGUSTUS with the meta parameters it has set.) from http://www.molecularevolution.org/molev ... ining.html. does it mean that interrupting the optimize_augustus.pl is not a big deal, you could still use the interrupting results to do downstream analysis (etraining --species=As As.genes.gb.train) ?
Thanks a lot,
Best,
Yafei
I am using optimize_augustus.pl to optimize my 'new' species. But It has been taking over six days on 24 CPU =-= importantly, the time will be out soon because I set the max running time is 6 days and 23 hours. So I have two confusions here, could you help me figure out^^?
my command line looks like:perl optimize_augustus.pl --species=As As.genes.gb.train
1. I did not set the option --cpus=24, so if I would not set the cpus number, dose the script only use 1 cpu?
2. As I describe above, The time will be out soon and the optimize_augustus.pl won't be finished, so, do any commands or scripts could continue the unfinished optimize training? And also, I found the cue (After optimize_augustus.pl has finished or (after you have interrupted it) you should (re)train AUGUSTUS with the meta parameters it has set.) from http://www.molecularevolution.org/molev ... ining.html. does it mean that interrupting the optimize_augustus.pl is not a big deal, you could still use the interrupting results to do downstream analysis (etraining --species=As As.genes.gb.train) ?
Thanks a lot,
Best,
Yafei