[mira_talk] Re: Parameters not parsed
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira talk <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 6 Apr 2009 16:31:32 +0200
Yeah, right, RTFM (although it's long).
It was much better using the parameters in the right order (placing my
pet specific switches after the --job one):
mira --project=x -fasta -job=denovo,genome,454,normal -OUT:ora=yes -
GE:not=4 -AS:urd=no > assembly_log.txt
Sorry for disturbing...
Lionel
On 6 Apr 2009, at 15:10 , Lionel Guy wrote:
Hi mira-friends
I tried to tweak the parameters a little bit, because I'm getting very
strange results with one of my assemblies. It seems that mira is
unwilling to parse my parameters (darn).
My project:
- sequencing a complete bacterial genome (~2Mb)
- half a 454 Titanium run (~100Mb of data, not quite as much as
advertised), plus 2 lanes from a titration run.
- about 50k paired-end mates (experimental 20kb library)
The bacteria that I'm sequencing experiences some kind of weird
alternate replication in late growth-phase, leading to an (at least) 2
fold amplification of about 10-20% of the genome, which may impair the
uniform read distribution (I tried with urd:yes, and yielded strange
results).
Here is some parts of the assembly_log:
<code>
-SB:sbuip is 3, but must be no more than 2. Setting to 2
</code>
Didn't say anything about strain or backbone... strange, but shouldn't
cause any problems...
<code>
Parsing parameters: --project=BAnh1NrPeM01 -fasta -OUT:ora=yes -
GE:not=4
-AS:urd=no --job=denovo,genome,454,normal
</code>
Fine, that's what I want. But then:
<code>
Parameter settings seen for:
Sanger data (also common parameters), 454 data
Used parameter settings:
General (-GE):
Project name in (proin) : BAnh1NrPeM01
Project name out (proout) : BAnh1NrPeM01
Number of threads (not) : 2
</code>
Uh? I said 4... But it's still OK...
<code>
Assembly options (-AS):
[...]
Automatic repeat detection (ard) : yes
[...]
Use uniform read distribution (urd) : yes
Start in pass (urdsip) : 5
Cutoff multiplier (urdcm) : [san] 1.5
[454] 1.5
</code>
Uh??? I asked not to use urd...
Any suggestion? Am I doing something wrong?
Thanks for your help... I might come here again to discuss my weird
assembly.
Lionel
Uppsala University
============================================
Lionel Guy
Thunmansgatan 25, SE-75421 Uppsala
phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy.lionel@xxxxxxxxx
============================================
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