I have assembled 2 >2.5G genomes (not the same, both mammals) in about 48hrs using 2025cores. This works great.
I'm trying to assemble a fish and I am having issues I don't quite know how to debug. The fish is about 1.9Gb in size and not diploid. If I run Ray using the paired + mates using k31 I was able to assemble it in 168hours (I needed to restart after 120hours because of walltime...thanks for the checkpoints :-) ). It worked (although the assembly wasn't great, possibly due to a lot of repeats), but took way longer than the bigger genomes. I'm trying the same without the mates. I also changed the kmer from k31 to k61. I hit walltime 5 times now, 120hours each and it's not finished. The variables that changed are kmer and no mates. The first run ran many steps in the log. Since the first wall time, the only output I seem to be having Rank X: gathering scaffold links [Y/2987] [Z/7166] (X,Y,Z varies of course) I was using a version compiled from sources for the polytope routing. Any ideas? Louis ------------------------------------------------------------------------------ LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
