[mira_talk] Re: Where is my assembly at?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 15 Sep 2011 23:57:16 +0200
On Sep 15, 2011, at 23:19 , Artemus Harper wrote:
> I started this up using screen, so I don't have the log fine saved anywhere.
Well, you will never, _never_, *never*, N.E.V.E.R. commit that error again to
start MIRA without redirecting the output to some file, will you? ;-) It might
have been extremely helpful here.
> Here is what I started with:
> mira_3.4.0_prod_linux-gnu_x86_64_static/bin/mira --project=Chemdawg_mira_1
> --job=genome,solexa SOLEXA_SETTINGS
> -FN:fqi=Medicinalgenomics.com_Prep7_1-1_sequences.txt
> -GE:tismin=150,tismax=400
Looks fine.
> According to the data in the tmp file, 42403 contigs were created in the
> first pass.
It does not tell you how many reads are left atm ... and you have at least a
further 4 passes to go. I'm sorry for being so brutal, but forgat that assembly
run.
> The input file contained 165481300 reads each had exactly 101 base pairs.
Holy crap! You put in an entire lane of HiSeq for MIRA? That's 3 to 5 times
more the amount of reads I currently feel comfortable to recommend MIRA for.
Can you please tell how big the genome is you're trying to assemble (or what
type? bacterium, lower or higher eukaryote, bacterial metagenome, etc.pp)? That
might give me a couple of clues.
B.
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