[mira_talk] Re: run time complications withmira_3.0.0_prod_linux-gnu_x86_64_static
- From: Susanne Franssen <susefranssen@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 3 Mar 2010 10:17:29 +0100
I have now run the assembly on my data
>I am using mira_3.0.0_prod_linux-gnu_x86_64_static for de nove EST
>assembly of a plant transcriptome. I have approximately 800.000 454
>titanium reads from an non-normalized cDNA library and I started the
>job with the following parameters:
with the cmd:
mira -project=name -job=denovo,est,draft,454 -notraceinfo (1)
and the changed parameters that you had suggested:
mira -project=JGI_ESTs_FK -job=denovo,est,draft,454 -notraceinfo
-SK:mnr=yes 454_SETTINGS: -CL:smrc=4 (2)
It, however; did not change the runtime:
9126m42.232s (1) vs 9011m30.624s (2)
nor the reads ending up as debris
90659 (1) vs 90076 (2)
... does thins mean know that the data set might not be as repetitive
after all, or what else could you conclude from that?
thanks, Susanne
On Sun, Feb 28, 2010 at 7:31 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Mittwoch 24 Februar 2010 Susanne Franssen wrote:
>> The cmd line was:
>> > mira -project=name -job=denovo,est,draft,454 -notraceinfo
>>
>> The job has now finally finished after all. I could rerun it again
>> though with the suggestions you gave me, especially when I want to do
>> it in the accurate mode. What exactly should this change with the
>> assembly results. I mean cpat had been on by default and the mnr
>> should result in more reads ending up in the debris possibly because
>> overlaps won't be assembled due to masked regions?!
>
> Yes, mnr will probably lead to more reads in the debris. But also to a
> reduction in time needed ... sometimes tremendously so.
>
> Regards,
> Bastien
>
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