On 21/07/11 16:52, Sébastien Boisvert wrote: > Can you send me (pastebin) the CoverageDistribution.txt file for each of your > runs. > I will add them to my unit tests.
It gets more weird. With the flush patch, Ray is able to attempt an assembly, presumably because coverage(0) < coverage(2): http://pastebin.com/mK6FGR2B Rank 0: the minimum coverage is 0 Rank 0: the peak coverage is 2 ... Number of contigs: 153 Total length of contigs: 49920 Number of contigs >= 500 nt: 29 Total length of contigs >= 500 nt: 19433 Number of scaffolds: 153 Total length of scaffolds: 49920 Number of scaffolds >= 500 nt: 29 Total length of scaffolds >= 500: 19433 Without the flush patch, Ray panics from a bad coverage distribution: http://pastebin.com/FqumBBFH Rank 0: the minimum coverage is 1 Rank 0: the peak coverage is 1 Rank 0: Assembler panic: no peak observed in the k-mer coverage distribution. Rank 0: to deal with the sequencing error rate, try to lower the k-mer length (-k) Rank 9: sent 203748 messages, received 203749 messages. Rank 8: sent 203487 messages, received 203488 messages. Rank 7: sent 204303 messages, received 204304 messages. Rank 6: sent 204861 messages, received 204862 messages. Rank 5: sent 203780 messages, received 203781 messages. Rank 4: sent 203762 messages, received 203763 messages. Rank 3: sent 203870 messages, received 203871 messages. Rank 2: sent 204344 messages, received 204345 messages. Rank 1: sent 204085 messages, received 204086 messages. Rank 0: sent 203614 messages, received 203604 messages. > Also, do you have a place where I could upload you data-for-unit-tests and > data-for-system-tests so that > you can run tests ? Unfortunately no. I have plenty of storage space on our Illumina server (and am expecting ~300TB sometime soon), can download as much as I want from here, but the internal network is not accessible from external sites (so I don't think I can set up an upload service). -- David ------------------------------------------------------------------------------ 5 Ways to Improve & Secure Unified Communications Unified Communications promises greater efficiencies for business. UC can improve internal communications as well as offer faster, more efficient ways to interact with customers and streamline customer service. Learn more! http://www.accelacomm.com/jaw/sfnl/114/51426253/ _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
