Question: Minia bug with "--debloom original"
0
gravatar for shammond
9 months ago by
shammond0
shammond0 wrote:

Hi Rayan/Devon,

I was assembling a set of 2x250 human reads with 72x coverage using the beta version of minia 3 that you kindly provided me, when I encountered this error:

[bug detected in adjacency data structure] was supposed to delete node AAAAAAAAAAAAAAAAAAAAAGGTCTGGGGTGTCATTATATTGCCCAGGCTGGTCTCAAACTCTTGGGCTCAAGTGATCCTCCCACCTTGGCCTCATAAGAGTGTTGGGATTACAGGCGTGAGCCACTGTGCCCGCCCTGTCTCTATTTATACAAATAAA but couldn't find it :(.
assembly may be inaccurate around this kmer. will continue assembling anyway

It occurs (with different nodes) 3822419 times at k 144 and 3682804 times at k 160, but never at k 128 or below. The only difference between these runs, aside from k, is that I used "--debloom original" at k > 128.

Perhaps because of this bug, the run time has increased from ~20 h to > 100 h, and the N50 has dropped from 5777 (k128) to 822 (k144).

Is there a fix for this bug?

Thanks, Austin

minia • 301 views
ADD COMMENTlink modified 9 months ago by Rayan Chikhi1.1k • written 9 months ago by shammond0
1
gravatar for Rayan Chikhi
9 months ago by
Rayan Chikhi1.1k
France, Lille, CNRS
Rayan Chikhi1.1k wrote:

No fix yet, I don't think I've tested that latest minia 3 on large genomes with k > 128 yet :) Thanks for pointing it out! Will let you know when a fix is out.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Rayan Chikhi1.1k
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