[mira_talk] Re: 454 walkthrough no quality data?
- From: Charles Determan Jr <deter088@xxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 14 Dec 2011 09:23:32 -0600
I have redone the sff_extract with the -Q parameter. I was previously
unaware of this option. This so far appears to have fixed the current
issue. I should have known I would need some other way to get the FASTQ
format. As for 'sudo', I have been making a document of any issues I have
and I used that a little while back when the directory was still assigned
to root. I have since changed ownership of the directory and not using
sudo. I understand the ramifications of using sudo and have made it so I
don't need it.
Regards,
On Mon, Dec 12, 2011 at 3:30 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Dec 12, 2011, at 20:29 , Charles Determan Jr wrote:
> > I am new to MIRA and have been trying to work through the walkthrough
> for the 454 data. I am able to use sff_extract and rename everything
> according to the document (except changing fasta to fastq format).
>
> You cannot change FASTA to FASTQ simply by renaming the files. But you can
> tell sff_extract to give you FASTQ directly: simply add "-Q" as parameter.
>
> > However, when I run the assembly with the command sudo /.../mira
> --project=bceti --job=denovo,genome,accurate,454 >&log_assembly, there are
> no results and the log file tells me there is no quality data. Any
> suggestions are thoughts for troubleshooting this would be truly
> appreciated. If you require further information or coding I have done, I
> can post that as well.
>
> Sending the log_assembly.txt file would actually help to see what you did.
>
> One thing however troubles me right away: "sudo"??? Why on earth are you
> using sudo?
>
> B.
>
>
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