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sebhtml / ray

Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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Checkpoints break extension produce shorter sequencers #116

Closed sebhtml closed 11 years ago

sebhtml commented 11 years ago

[boisver1@ip03 eel-Ray-2012-12-12-3]$ grep reached eel-Ray-2012-12-12-3.1.0183|head Rank 183 reached 0 vertices from seed 0, flow 1 Rank 183 reached 1000 vertices from seed 0, flow 1 Rank 183 reached 2000 vertices from seed 0, flow 1 Rank 183 reached 3000 vertices from seed 0, flow 1 Rank 183 reached 3393 vertices from seed 0, flow 1 Rank 183 reached 0 vertices from seed 0, flow 2 Rank 183 reached 1000 vertices from seed 0, flow 2 Rank 183 reached 2000 vertices from seed 0, flow 2 Rank 183 reached 3000 vertices from seed 0, flow 2 Rank 183 reached 3393 vertices from seed 0, flow 2 [boisver1@ip03 eel-Ray-2012-12-12-3]$ grep reached ../eel-Ray-2012-12-10-2/eel-Ray-2012-12-10-2.1.0183|head Rank 183 reached 0 vertices from seed 0, flow 1 Rank 183 reached 1000 vertices from seed 0, flow 1 Rank 183 reached 2000 vertices from seed 0, flow 1 Rank 183 reached 3000 vertices from seed 0, flow 1 Rank 183 reached 4000 vertices from seed 0, flow 1 Rank 183 reached 5000 vertices from seed 0, flow 1 Rank 183 reached 6000 vertices from seed 0, flow 1 Rank 183 reached 7000 vertices from seed 0, flow 1 Rank 183 reached 8000 vertices from seed 0, flow 1 Rank 183 reached 9000 vertices from seed 0, flow 1

Without checkpointing: Rank 183 starts on seed 0, length is 3393, flow 0 [0/3293] Current peak coverage -> 147

With checkpointing: Rank 183 starts on seed 0, length is 3393, flow 0 [0/3293] Current peak coverage -> 1

So something is missing in the checkpoint files for seeds.

sebhtml commented 11 years ago

4987d09ef38e11a6f2d6ccbd61371e68b25addac