I've tried to assemble 360 million single end reads (not with ray, but with IDBA_UD) on a machine with 320 GB, and that (incl. swap) was not enough (with default settings) -> doubt you have enough memory on your current system.
Tried recently another assembler (Megahit), which managed to do it (with default settings), might want to try that. ________________________________ From: Rika Anderson <rikan...@u.washington.edu> Sent: Monday, May 18, 2015 22:32 To: denovoassembler-users@lists.sourceforge.net Subject: [Denovoassembler-users] long running time for metagenome assembly on Ray Hello, I'm trying to do a large co-assembly of 10 metagenomes using Ray (I know that running them individually would be faster; but for our purposes we want to do a co-assembly if possible). I have overlapping paired-end reads that have been merged and filtered, yielding a total of about 632 million single-end reads of about 150bp in length for all 10 samples. I have tried running Ray on this dataset using n = 80 and k = 31 on a cluster with 40 (80 hyperthread) cores and 256 GB memory, and according to the log there are at least 35 days remaining for the k-mer counting step. The network testing step reported an average node latency of 205.6 and a standard deviation of 63.9002 for all ranks. So my question is: is this kind of time frame normal for a dataset of this size and on this kind of computer network? Running for over 30 days for a dataset that's about 600 million non-paired reads seems like a lot. Am I doing something wrong, or is there anything I can do to reduce the running time? We have another general-use cluster with 32 cores and 1024 GB memory; would running it on that cluster work better because of higher memory availability? Thanks for any advice! Best, Rika Anderson -- Rika Anderson, Ph.D. NASA Postdoctoral Fellow NASA Astrobiology Institute ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
