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From: Sébastien B. <seb...@ul...> - 2011-07-13 16:17:43
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Can you report this to denovoassembler-devel ? https://lists.sourceforge.net/lists/listinfo/denovoassembler-devel (should be up in a few) When you post to denovoassembler-devel, can you paste CoverageDistribution.txt on pastebin and link it in your email. By the way: message maximum length on the mailing list is 65536 bytes, lengths above are rejected. Also: on which data are you testing ? This may help you: (1) For developing new code in Ray, I use assertions. So when you see ifdef ASSERT, the codes inside of these bits are not for production but just used for development. For instance, if you read structures/MyHashTable.h or memory/DefragmentationGroup.cpp, you will see a lot of them. (2) Unit tests are in unit-tests bash main.sh runs the unit tests. (3) System tests are in system-tests data-for-system-tests are not in the git repository I can upload these bits to a system of yours if you want. then you must create a symbolic link as follows: /rap/nne-790-ab/data-for-system-tests -> actual place where is data-for-system-tests To run system tests on a SMP computer: cd system-tests ./main-smp.sh To run system tests with Sun Grid Engine: cd system-tests ./main-sge.sh Sébastien > ________________________________________ > De : David Eccles (gringer) [dav...@mp...] > Date d'envoi : 13 juillet 2011 07:27 > À : den...@li... > Objet : Re: [Denovoassembler-users] Confused about coding -- completed seeds without distributions > > On 12/07/11 16:49, David Eccles (gringer) wrote: >> However, the code I have doesn't seem to have any success in finding seeds. > > I added a bit of debugging output, and came up with this: > > Rank 0 is selecting optimal read markers [1/1000] > inserting sequence (0): T0312332212212032313211021010112303320130220032131 > inserting sequence (1): T0230102032123100220032121302331231100332020012031 > inserting sequence (2): T2102202120200310123200323013323110122001100012320 > inserting sequence (3): C1312102002001322010320202013210121223010123122033 > inserting sequence (4): A2121223331021020132132300201223202232300220310201 > ... > Rank 0 is creating seeds [1/10020] > Vertex 1-1 test (4): testing C21012121330003101031 > Vertex 1-1 test (5): testing C13010130003312121012 > Vertex 1-1 test (6): testing A33102002200001000130 > Vertex 1-1 test (7): testing T03100010000220020133 > Vertex 1-1 test (8): testing G23300202002023312231 > Vertex 1-1 test (9): testing A13221332020020200332 > ... > Vertex 1-1 test (8168): testing T31233221221203231321 > ... > Continuing (8168): vertex has 1 in, 1 out: T31233221221203231321 > Vertex 1-1 test (8168): testing T03123322122120323132 > ... > Finished (8168): parent has 1 in, 1 out: T03123322122120323132 > worker 8168 done: found a seed with 20 nucleotides > > [workerIds are in brackets] > > So this seed (T31233221221203231321) is rejected, because there's a > parent vertex (T03123322122120323132) that is closer to the start of the > sequence. Except that parent vertex is never processed, it's nowhere in > my output. Note that the first workerId is 4, not 0. I have a suspicion > that the wonderful "ultimate first seed" is something that should be > managed by worker 0, who decided to take a holiday. > > This probably might not be a problem for imperfect reads, because you'd > expect breaks in the chain somewhere (so at least *some* sequence would > map properly, even if the first workers weren't processing). I think the > problem here is that all vertices are linked to this first one. > > I still need to hunt more, but I think I'm getting close to the problem. > > --- David > > > ------------------------------------------------------------------------------ > AppSumo Presents a FREE Video for the SourceForge Community by Eric > Ries, the creator of the Lean Startup Methodology on "Lean Startup > Secrets Revealed." This video shows you how to validate your ideas, > optimize your ideas and identify your business strategy. > http://p.sf.net/sfu/appsumosfdev2dev > _______________________________________________ > Denovoassembler-users mailing list > Den...@li... > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > |
