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 Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users