[mira_talk] Re: Mapping a sequence with MIRA
- From: Federico Sanchez <federicosq@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Mar 2010 12:30:58 +0100
Hi:
Thanks for the quick answer. I just did what you suggeested me. and change
the files to the _in.454.fasta format, for all of them (the quality file and
the backbone too). However I am still getting an error with the backbone
file --->
Fatal Error (may be due to problems of the input data):
"File not found: 454_muestra2_backbone_in.fasta"
->Thrown: size_t ReadPool::loadDataFromFASTA(const string & filename, const
uint8 loadaction, uint32 & longestread, const bool wantsqualfiletoexist,
const string & qualfilename, const bool generatefilenames, const uint8
seqtype, const bool sxa_mustconvert)
->Caught: main
Program aborted, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
CWD: /home/homes/users/fsanchez/MIRA_ASSEMBLY
Aborted
My command line is the same but changing the backbone file to
backbone_in.454.fasta instead of the 454_muestra2_backbone_in.fasta, what
else could be going wrong? any suggestions?. At the moment I am not able to
download the newer versions of mira but I hope mira 3.0.0 is up for the
task.
/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.454.fasta:bbq=100:bft=fasta:abnc=yes
Thanks again for the help
Federico
On Mon, Mar 15, 2010 at 11:36 AM, Jan Paces <hpaces@xxxxxxxxxx> wrote:
> On 03/15/10 04:56, Federico Sanchez wrote:
> > 1) /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
>
> For mapping, I suggest to use mira-3.0.3, there were some problems with
> parsing input data in version 3.0.2 a maybe lower as well, I am not sure.
>
> As for the error with input files, you need _in.454. in the names -
> as pointed out by Sven befora I sent this email ;-)
>
> Jan
>
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