[mira_talk] Re: run time complications withmira_3.0.0_prod_linux-gnu_x86_64_static

  • From: Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 03 Mar 2010 10:43:22 +0100

-- Hi Susanne,
i use the same version of mira to assemble 454 reads and it's work fine for me with good results. 
this is the command line i use:
bin/mira -project=trimmed_NG-5114_Hemo_sequence -fasta=trimmed_NG-5114_Hemo_sequence.fna -job=denovo,est,normal,454 -notraceinfo COMMON_SETTINGS -GENERAL:kcim=yes,not=4 -CL:pec=no -SK:mnr=yes,nrr=8,mmhr=6 -CO:asir=yes,mr=no 454_SETTINGS -LR:wqf=no -CO:fnicpst=yes,rodirs=10 -CL:cpat=no,pvlc=no,qc=no,bsqc=no,mbc=no,emlc=yes,mlcr=0,smlc=0,emrc=yes,mrcr=0,smrc=0 -OUT:sssip=no -AL:bip=5,bmin=10,mrs=98:egp=yes:egpl=reject_codongaps:megpp=100,mo=60 -AS:mrl=30,bdq=30,epoq=no
for example with 579491 reads on my server(HP ProLiant DL585-G2, 4x Dual-Core AMD Opteron Processor 8216 @ 2400MHz, 64GB RAM, CentOS release 4.6) it takes 
24 hours to finish job.

Laurent --


Susanne Franssen a écrit :

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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