[mira_talk] Re: mira 3.9 manifest file for hybrid assembly
- From: Marcelo Brandão <brandao.marcelo@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 19 Oct 2012 13:51:22 -0300
Hi there
I am trying to run mira 3.9.4 but I am getting the following error when try
to map solexa reads over 454 assembly:
Fatal error (may be due to problems of the input data or parameters):
"While trying to load data for readgroup, type caf not known."
Is there some workaround on how to use caf files, or should i use another
file format?
Thanks
Marcelo
2012/10/13 Marcelo Brandão <brandao.marcelo@xxxxxxxxx>
> Wow,
> Thanks Bastien, I do not realise that I need this. I will try it and post
> the result here.
> Happy weekend!
> Marcelo
>
> 2012/10/12 Bastien Chevreux <bach@xxxxxxxxxxxx>
>
>> On Oct 12, 2012, at 23:16 , Marcelo Brandão wrote:
>>
>> [...]
>> "In file ../map3_manifest.dat: line
>> -SK:mnr=1:pr=70:hss=2
>> has keyword '-sk:mnr' which is not recognised."
>>
>>
>> Ah, I see. You forgot the backslashes at the end of the parameter lines.
>> From the manual:
>>
>> Note
>>
>> For improved readability, you can distribute parameters across several
>> lines either by pre-fixing every line with parameter=, like so:
>>
>> job=denovo,genome,draft
>> parameters= 454_SETTINGS -AS:mrl=80:bdq=10
>> parameters= SOLEXA_SETTINGS -AS:mrl=30:bdq=15
>>
>> Alternatively you can use a backslash at the end of a parameter line to
>> indicate that the next line is a continuing line, like so:
>>
>> job=denovo,genome,draft
>> parameters= 454_SETTINGS -AS:mrl=80:bdq=10 *\*
>> SOLEXA_SETTINGS -AS:mrl=30:bdq=15
>>
>>
>> Note the backslash in the second version.
>>
>> B.
>>
>>
>
>
> --
> Marcelo Mendes Brandão
> Academic Visitor at University of Alberta @ Edmonton
> Website: http://bioinfo.esalq.usp.br
> AtPIN: http://bioinfo.esalq.usp.br/atpin
> SKYPE: mmbrand
>
--
Marcelo Mendes Brandão
Academic Visitor at University of Alberta @ Edmonton
Website: http://bioinfo.esalq.usp.br
AtPIN: http://bioinfo.esalq.usp.br/atpin
SKYPE: mmbrand
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