[mira_talk] Re: Parameters not parsed

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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