On 13/07/11 17:01, David Eccles (gringer) wrote:
> Um... what? So... the first few workers that get added don't actually do
> any work, and the activeWorkers array isn't populated until the first 5
> vertices are loaded. This agrees with what's on lines 138-144:
>
> int coverage=node->getCoverage(&vertexKey);
> int minimum=5;
> if(coverage<minimum){
> m_completedJobs++;
> }else{
> m_aliveWorkers[m_SEEDING_i].constructor(&vertexKey,m_parameters,
> m_outboxAllocator,m_virtualCommunicator,m_SEEDING_i);
> m_activeWorkers.insert(m_SEEDING_i);
> }
If I reduce that minimum down to 2 [i.e. changing
that-which-should-not-be-changed], and change one of the output strings
to base-space [it was previously displaying the root k-mer in
colour-space], then I get a successful assembly, both for sebhtml/ray,
and for gringer/ray.
$ wc -l test_phiX.Contigs.fasta testSeb_phiX_5k.Contigs.fasta
90 test_phiX.Contigs.fasta
90 testSeb_phiX_5k.Contigs.fasta
180 total
$ diff test_phiX.Contigs.fasta testSeb_phiX_5k.Contigs.fasta
[no output]
$ fasta_formatter -i ../tests/phix/phix.fasta | fastx_reverse_complement
| grep $(fasta_formatter -i test_phiX.Scaffolds.fasta | grep -v '^>') >
/dev/null && echo "success (match in reverse direction)"
success (match in reverse direction)
My code now does a correct assembly both on simulated and on real
(circularised) phiX data:
$ ../code/Ray -s
~/illuminadata/110517_H134_0062_A816HKABXX/Data/Intensities/BaseCalls/fastq/ignore/head100k_interleaved_noN_phiX_region1101.fasta
-o ray_output/test2_phiX_circular
...
Number of contigs: 1
Total length of contigs: 5385
Number of contigs >= 500 nt: 1
Total length of contigs >= 500 nt: 5385
Number of scaffolds: 1
Total length of scaffolds: 5385
Number of scaffolds >= 500 nt: 1
Total length of scaffolds >= 500: 5385
-- BLAST results (for 600bp sequence overlapping joiner) --
>gb|M14428.1|S13CG Bacteriophage S13 circular DNA, complete genome
Length=5386
Score = 1068 bits (1184), Expect = 0.0
Identities = 597/600 (99%), Gaps = 0/600 (0%)
Strand=Plus/Plus
$ ./test_phiX.sh
Checking full Ray run with phiX genome... 5000 Reads simulated...
Running Ray... success (match in forward direction)!
This is doing things that Ray can already do (i.e. read in base-space
reads, assemble, output as base-space), but I need to make sure it can
do at least that before trying other things.
It's also slower than sebhtml/ray (Total: 25 seconds vs 14 seconds; 57
seconds if I include asserts and debug symbols). I presume this is
because of the additional complexity for getOutgoingEdges / getLastCode
(it needs to re-calculate the last base each time by iterating through
the k-mer). Perhaps the k-mer should store the last base as well as the
first....
-- David
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