[mira_talk] Re: Fishy tag
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 16 Feb 2011 21:46:35 +0100
On Wednesday 16 February 2011 21:25:05 Louis Letourneau wrote:
> I'm a new user of mira so please bear with me.
>
> I have 2 sets of Illumina paired 76 reads that are from a bacterial
> strain. I want to find variations(snp, structural the works) between
> them. They are pretty close to a sequenced strain found in refseq at NCBI.
>
> So, following the nice examples in the documentation, I downloaded the
> genbank file and tried to align to it.
>
> mira want's nothing to do with the file. I get a lot of:
> "Fishy tag (to is greater than sequence length of 0):"
>
> And in the end it stops with:
> Internal logic/programming/debugging error (*sigh* this should not have
> happened).
> Please file a bug report on
> http://sourceforge.net/apps/trac/mira-assembler/
>
> "NC_007793: tag to (0) >= len of sequence (0)?"
>
> ->Thrown: void Read::addTag(tag_t & tag)
> ->Caught: void setTags(const vector<tag_t> & tags)
>
> Aborting process, probably due to an internal error.
Hello Louis,
hmmm, I just downloaded Saur NC_007793 from NCBI and used it without problems
as backbone.
However, I think I remember having fixed a bug lately which made MIRA puke
(with exactly the symptoms you describe) when the file somehow first passed via
a Windows/DOS environment and had the DOS style of line feeds.
You have two options:
1) try out a current development version of MIRA (3.2.1.5), where this bug is
fixed. For that, head to
http://sourceforge.net/projects/mira-assembler/files/MIRA/development/
2) convert the DOS format of the GenBank file to Unix format. I'd use dos2unix
or a number of other available tools for this.
http://kb.iu.edu/data/acux.html
gives a good overview
Please tell if that helped (or not).
B.
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