[wgs-assembler-users] huge assembly with thousands of MergeScaffoldsAggressive iterations

[kuhl <ku...@mo...>]

Hi Brian et al.,

I am currently running a huge assembly with CA7 (2.5Gb 30x Illumina + 454,
cgw takes 150-300Gb RAM). It is now in step 7-2 and I have just stopped cgw
at MergeScaffoldsAggressive iteration 1641 and restarted it at ckp08-2SM. I
did this also in 7-0 at iteration 2xxx. Now I am not sure, if I should
maybe rerun scaffolding without 20 kb mate pairs, which I think are
responsible for this mess. So I have two questions: 

How can I convince cgw to ignore a certain library without doing steps 0-5
again? 

Is there a rule of thumb, when MergeScaffoldsAggressive should be stopped?


In my case it looks like cgw is only very slightly progressing with each
iteration and there is one large scaffold that is growing more and more...

ExamineUsableSEdges()- maxWeightEdge from 0 to 32 at idx 3355 out of 60498
ExamineUsableSEdges()- maxWeightEdge from 0 to 19 at idx 8774 out of 60498
ExamineUsableSEdges()- maxWeightEdge from 0 to 55 at idx 286 out of 60500
ExamineUsableSEdges()- maxWeightEdge from 0 to 32 at idx 3355 out of 60500
ExamineUsableSEdges()- maxWeightEdge from 0 to 16 at idx 10594 out of
60500
ExamineUsableSEdges()- maxWeightEdge from 0 to 7 at idx 20348 out of 60500
ExamineUsableSEdges()- maxWeightEdge from 0 to 55 at idx 286 out of 60489
ExamineUsableSEdges()- maxWeightEdge from 0 to 32 at idx 3355 out of 60489
ExamineUsableSEdges()- maxWeightEdge from 0 to 19 at idx 8773 out of 60489
ExamineUsableSEdges()- maxWeightEdge from 0 to 9 at idx 16854 out of 60489
ExamineUsableSEdges()- maxWeightEdge from 0 to 55 at idx 286 out of 60486
ExamineUsableSEdges()- maxWeightEdge from 0 to 32 at idx 3355 out of 60486
ExamineUsableSEdges()- maxWeightEdge from 0 to 16 at idx 10593 out of
60486
ExamineUsableSEdges()- maxWeightEdge from 0 to 7 at idx 20428 out of 60486

Regards, Heiner