[mira_talk] Re: MIRA disk space issue
- From: Arun Rawat <rawat_arun@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 15 Apr 2011 11:56:18 -0700 (PDT)
I think the mapping is less intensive than denovo.
Did you had any chance to look at your log output. I once ran incompatible mira
in IA-64 architecture and it bloated the log file quickly into several gb in
matter of minutes. See if something similar is happening to you,
Arun
----- Original Message ----
From: Leonor Palmeira <mlpalmeira@xxxxxxxxx>
To: mira_talk@xxxxxxxxxxxxx
Sent: Fri, April 15, 2011 6:43:22 AM
Subject: [mira_talk] Re: MIRA disk space issue
Hi,
why don't you use both the 454 and Illumina reads and do a full hybrid assembly
instead of mapping the Illumina reads on your previous 454 scaffolds? I think
it
would be the most appropriate approach to handle your data with MIRA.
I also don't think you would get to the space disk issue you are mentioning,
but
I might be wrong.
Best,
Leonor.
On 15/04/11 15:33, Marco Fondi wrote:
> Hello!
> I'm using Mira for a de novo sequencing project. At this stage of the project
> I
>have both some 454 scaffolds (coming from a Paired End run) and some (5000000)
>Illumina reads coming from a later run. Now, I want to go further with this
>assembly, trying to map the Illumina reads on the scaffolds and having extra
>contig from Illumina reads that cannot be mapped on the scaffolds. Everything
>is
>ok at the beginning but, in a few hours, all the space on my disk (almost 80G)
>is over and, of course, the assembly stops. I have tried several times and
>changing a little bit the command line parameters but I got always the same
>result. Do you have some idea on how to fix this? Is this a known issue and I
>simply need more disk space available for MiRA to work?
> Thanks in advance.
> cheers,
> m.
>
>
> Marco Fondi, PhD
> LEMM (Lab. of Molecular and Microbial Evolution)
> Dep. of Evolutionary Biology
> University of Florence
> Via Romana 17/19, 50125 Firenze
> tel. 055 2288248
> fax 055 2288250
> skype: marco.fondi
> web: http://www.unifi.it/dblemm/CMpro-v-p-1.html
> flickr: http://www.flickr.com/photos/_m1/
>
>
-- Leonor Palmeira, PhD
Phone: +32 4 366 42 69
Email: mlpalmeira AT ulg DOT ac DOT be
http://sites.google.com/site/leonorpalmeira
Immunology-Vaccinology, Bat. B43b
Faculty of Veterinary Medicine
Boulevard de Colonster, 20
University of Liege, B-4000 Liege (Sart-Tilman)
Belgium
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