[mira_talk] Re: Where is my assembly at?
- From: Artemus Harper <subanark@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 15 Sep 2011 14:19:26 -0700
I started this up using screen, so I don't have the log fine saved anywhere.
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
According to the data in the tmp file, 42403 contigs were created in the
first pass. The input file contained 165481300 reads each had exactly 101
base pairs.
On Thu, Sep 15, 2011 at 1:53 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Sep 15, 2011, at 19:04 , Artemus Harper wrote:
> > I've been running mira for a few weeks now. I think its done with pass 1,
> but I'm not sure what it is doing now, or how much longer it has.
> > The last few lines are (and its been doing this for at least a couple of
> days now):
> >
> > [314880] ++aaaaaaaaaaa+aaa+aaa+aaaaaaaaa+aa++aaaaaaaaaaaaaaaaaaaaaaa+
> 11683 329647 / 9208 / 20452
> > [314889] +aaaaaaaaaaaaaaaaaaaaaaa+aa+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
> 11683 357706 / 9245 / 29577
> > [314892] aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+aaaaaaaaaaaaaaaaaaaaaaa
> 11683 391095 / 10903 / 28012
>
> Oh my. This does not look sane ... not at all. If you're still in pass 1,
> then that assembly is very probably a lost cause.
>
> Can you please post the, say, first 5000 lines of the log file?
>
> B.
>
>
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--
Artemus Harper
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