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From: Sébastien B. <seb...@ul...> - 2011-07-21 15:45:05
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Patch work should only be on -devel please ! > ________________________________________ > De : David Eccles (gringer) [dav...@mp...] > Date d'envoi : 21 juillet 2011 11:35 > À : Sébastien Boisvert > Cc : den...@li... > Objet : Re: RE : [Denovoassembler-users] No observed peak in coverage distribution (454 test data) > > 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 > Sébastien |
