How to run wtzmo parallelly

[ruanjue]

How to run wtzmo parallelly

[ruanjue]

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

[Jolvii85]

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

[ruanjue]

It is ok, spliting reads will change the k-mer table, and result in some difference.