Comments (3)
wtzmo -P 10 -p 0 ...
wtzmo -P 10 -p 1 ...
...
wtzmo -P 10 -p 9
If run parallely, each job will take the same memory with standalone.
As you are assembling 20G genome, please have a try with wtdbg2 (v2.3), which is designed to handle huge genomes.
Jue
from smartdenovo.
Hi,
I use a small genome to test the wtzmo command. I combined the results of all wtzmo results, then run wtclp, the row number of obt file i got from here is the same with that non-parallelly run, but there are some disaccordance results (after sort each obt file), is it ok? there are 4300 lines, 16 are different (See below).
I test the whole pipeline, I found that if I parallelly run the wtzmo, the length of the assembly is similar with that of the non-parallelly run, but the no. of the scaffold is a little higher.
3136c3136
< pb000000003137 0 0 46937 0 0 1
---
> pb000000003137 0 46937 46937 0 46937 0
3433c3433
< pb000000003434 0 32304 32304 0 32304 0
---
> pb000000003434 0 0 32304 0 0 1
3557c3557
< pb000000003558 0 0 66886 0 0 1
---
> pb000000003558 0 66886 66886 0 66886 0
3764c3764
< pb000000003765 0 43177 43177 0 43177 0
---
> pb000000003765 0 0 43177 0 0 1
4001c4001
< pb000000004002 0 30644 30644 0 30644 0
---
> pb000000004002 0 0 30644 0 0 1
4018c4018
< pb000000004019 0 31422 31422 0 31422 0
---
> pb000000004019 0 0 31422 0 0 3
4044c4044
< pb000000004045 0 30629 30629 0 30629 0
---
> pb000000004045 0 0 30629 0 0 2
from smartdenovo.
It is ok, spliting reads will change the k-mer table, and result in some difference.
from smartdenovo.
Related Issues (20)
- Died at ./smartdenovo-master/smartdenovo.pl line 23. HOT 6
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- how to adjusting parameters to improve the assembly result HOT 3
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from smartdenovo.