[mira_talk] Re: 454 assembly with Mira
- From: Pau Corral <pau.corral@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 27 Nov 2011 20:09:08 +0100
Hi Christoph,
Regarding the command you use with python to extract the sequences and the
ancilliary file, you wrote:
python ~/scripts/sff_extract_0_2_10 -Q -s 454assembly_in.454.fastq -x
454assembly_traceinfo_in.454.xml FX37IYI01.MID1.sff FX37IYI02.MID1.sff
it is ok, you obtain a concatenation of the output files from your *.sff
files (two *.fastq concatenated and two *.xml concatenated)
Regarding the version you are using (MIRA 3.2.1) and the command to execute
it, you wrote:
mira --project=454assembly --job=denovo,genome,accurate,454
In here, you have to specify what type of input data you are passing to the
programe. As long as you are working with fastq, in MIRA 3.2.1 you might be
good to go with this:
mira --project=454assembly --job=denovo,genome,accurate,454 --fastq
cheers!
Pau
On Sun, Nov 27, 2011 at 7:38 PM, Christoph Hahn <chrisi.hahni@xxxxxxxxx>wrote:
> Thanks! Will try to convince the cluster administrator to update to v 3.4.
>
> cheers,
> Christoph
>
>
> On 11/27/2011 06:51 PM, John Nash wrote:
>
>> On 2011-11-27, at 12:33 PM, Christoph Hahn<chrisi.hahni@xxxxxxxxx>
>> wrote:
>>
>> Mira then stops after a while, saying the following (the complete stdout
>> can be found below):
>>
>>> Loading data (454) from FASTA files,
>>>>
>>>> Fatal error (may be due to problems of the input data or parameters):
>>>>
>>>> "File not found: 454assembly_in.454.fasta"
>>>>
>>> I guess I have to somehow specify to use the *fastq file instead of
>>> *.fasta. Or I am doing something else wrong. Can anyone help me?
>>>
>>> Much obliged!
>>> Christoph
>>>
>>> This is MIRA V3.2.1 (production version).
>>>>
>>>>
>> You are using an old version of Mira. Update to 3.4 and all should be
>> fine.
>>
>
>
> --
> You have received this mail because you are subscribed to the mira_talk
> mailing list. For information on how to subscribe or unsubscribe, please
> visit
> http://www.chevreux.org/mira_**mailinglists.html<http://www.chevreux.org/mira_mailinglists.html>
>
Other related posts:
