[mira_talk] Re: Mapping a sequence with MIRA
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Mar 2010 21:40:25 +0100
On Montag 15 März 2010 Federico Sanchez wrote:
> 2) /aplic/mira-3.0.0/bin/mira -fasta -project=454_muestra2
> -job=mapping,genome,normal,454 --noclipping=all --notraceinfo
> COMMON_SETTINGS -AS:sd=yes -SK:mnr=no
> -SB:lb=yes:bsn=454_muestra2_backbone_in.fasta:bbq=100:bft=fasta:abnc=yes
> -FN:fai=454_muestra2_in.fasta:fqui=454_muestra2_in.fasta.qual
>
>
> ========================= Parameter parsing error(s)
> ==========================
>
> * Parameter section: '-FN'
> * Parameter '454_muestra2_in.fasta' can only be set as sequencing type
> specific
> * parameter (SANGER_SETTINGS, 454_SETTINGS, etc.pp)
> * and not for COMMON_SETTINGS.
>
> * Parameter section: '-FN'
> * Parameter '454_muestra2_in.fasta.qual' can only be set as sequencing
> type specific
> * parameter (SANGER_SETTINGS, 454_SETTINGS, etc.pp)
> * and not for COMMON_SETTINGS.
>
> ===========================================================================
> ====
>
> Fatal Error (may be due to problems of the input data):
> "Error while parsing parameters, sorry."
MIRA tells you that setting the file names must be done in the sections which
are specific to the sequencing parameters as you can set different input files
for every sequecing technology.
You did:
mira
...
COMMON_SETTINGS
...
-FN:fai=454_muestra2_in.fasta:fqui=454_muestra2_in.fasta.qual
and MIRA will not know for which sequencing tech you want to set the file
names. In your case it's 454, so the correct way to do this would be:
mira
...
COMMON_SETTINGS
...
454_SETTINGS
-FN:fai=454_muestra2_in.fasta:fqui=454_muestra2_in.fasta.qual
Regards,
Bastien
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