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From: Sébastien B. <seb...@ul...> - 2011-07-14 14:21:13
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Works fine on my branch master. Commands: ~/git-clones/ray/readSimulator/VirtualNextGenSequencer ~/data-for-system-tests/phix/phix.fasta 0 200 10 500000 50 phix_500k_1.fasta phix_500k_2.fasta mpirun -np 3 ~/Ray -p phix_500k_1.fasta phix_500k_2.fasta |tee 1 Result: Number of contigs: 1 Total length of contigs: 5384 Number of contigs >= 500 nt: 1 Total length of contigs >= 500 nt: 5384 Number of scaffolds: 1 Total length of scaffolds: 5384 Number of scaffolds >= 500 nt: 1 Total length of scaffolds >= 500: 5384 Your distribution has 2 peaks. http://imgur.com/WoksH Should be like: http://imgur.com/lm84R Distribution: http://pastebin.com/qmJtWqj9 k-mer length: 21 Lowest coverage observed: 98 MinimumCoverage: 98 PeakCoverage: 5779 RepeatCoverage: 11460 Number of k-mers with at least MinimumCoverage: 10732 k-mers Estimated genome length: 5366 nucleotides Percentage of vertices with coverage 98: 0.0186359 % DistributionFile: RayOutput.CoverageDistribution.txt Did you provide the good input files ? Sébastien > ________________________________________ > De : Eccles, David [dav...@mp...] > Date d'envoi : 14 juillet 2011 02:48 > À : Sébastien Boisvert; den...@li... > Objet : RE: RE : Confused about coding -- completed seeds without distributions > > From: Sébastien Boisvert [mailto:seb...@ul...] >> VirtualNextGenSequencer dumps pairs of reads so you should provide both. >> Can you rerun with -p tests/phix/phix_500k_1.fasta > tests/phix/phix_500k_2.fasta >> Otherwise I think your graph won't be connected enough because of the > random number generator used to simulate reads. > > Okay, done. Coverage: > > http://pastebin.com/p6v7m1jA > > And output: > > http://pastebin.com/rEjqveCz > > Still failing to assemble. > > I must say that these results surprised me, because the minimum coverage from > Coverage Distribution has bumped up to 96 now. > >> Also, what is the read length ? > > Reads were generated using this command: > ../readSimulator/VirtualNextGenSequencer tests/phix/phix_genome.fasta 0 200 > 10 500000 50 phix_500k_1.fasta phix_500k_2.fasta > > In other words, no sequence errors, 200bp outer distance (SD = 10bp), 50bp > read length. I chose those outer distance / read length values (but SD was a > guess) because they are the same as the parameters used on a human genome > sequence that was done at MPI a month or so ago (which included a phiX lane). > I guess I could choose the reads from that as input, but then I'd be testing > a different thing, because those reads would likely have errors. > >> I added a system test for phiX and it works just fine on my branch master. >> see system-tests/tests/phix > > You're simulating errors / SNPs (substitution rate = 0.005), which is a > different test from the one I'm doing. > > -- David > |
