[mira_talk] Re: Fishy tag
- From: Louis Letourneau <louis.letourneau@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 16 Feb 2011 15:51:47 -0500
I just checked and the file is already in unix format, I ran dos2unix
anyways and same problem occured.
I'll try the development version.
Thanks for the quick reply!
By the way, you have one of the most complete documentation of any
opensource|(and many closed source) bioinformatics tool I've ever seen.
My hat's off to you Sir :-)
Louis
On 11-02-16 03:46 PM, Bastien Chevreux wrote:
> 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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