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landmark not recognized error on valid gff

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landmark not recognized error on valid gff

Mark

Hi

 

I’ve been trying repeatedly to load a sample gff3 file (which I validated at http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online) into webgbrowse but always get

 

“The landmark named NC_004353:1..1000 is not recognized. See the help pages for suggestions.”

 

I’ve attached my gff file.

 

Can you help me?

 

Thanks

 

Mark

 

 




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Re: landmark not recognized error on valid gff

Scott Cain
Hi Mark,

While that is valid GFF, it doesn't have anything that identifies what
NC_004353 is.  The reason that is still valid is that you might have
another GFF file that you loaded where it is defined, so an individual
GFF file can not have it and still be valid.  The best way to identify
the reference sequence is to add another GFF line:

NC_004353   .   contig   1   1234567    .    .    .    Name=NC_004353

where 1234567 is the length of the sequence.

Scott


On Mon, Feb 11, 2013 at 10:31 AM,  <[hidden email]> wrote:

> Hi
>
>
>
> I’ve been trying repeatedly to load a sample gff3 file (which I validated at
> http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online) into webgbrowse
> but always get
>
>
>
> “The landmark named NC_004353:1..1000 is not recognized. See the help pages
> for suggestions.”
>
>
>
> I’ve attached my gff file.
>
>
>
> Can you help me?
>
>
>
> Thanks
>
>
>
> Mark
>
>
>
>
>
>
>
> ________________________________
> This message may contain confidential information. If you are not the
> designated recipient, please notify the sender immediately, and delete the
> original and any copies. Any use of the message by you is prohibited.
>
> ------------------------------------------------------------------------------
> Free Next-Gen Firewall Hardware Offer
> Buy your Sophos next-gen firewall before the end March 2013
> and get the hardware for free! Learn more.
> http://p.sf.net/sfu/sophos-d2d-feb
> _______________________________________________
> Gmod-webgbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: landmark not recognized error on valid gff

Ram Podicheti-2
In reply to this post by Mark
<base href="x-msg://63/"> Mark,
GBrowse requires the seqID to be defined in the gff3 file as a separate entry. Try entering an additional line in your GFF3 file something like this.

NC_004353 . contig 1 51854 . . . ID= NC_004353;Name= NC_004353

Notice there are 9 columns each separated by a tab. 51854 is the length of the sequence. Let me know if you encounter more issues.
Cheers,

Ram

On Feb 11, 2013, at 10:31 AM, <[hidden email]>
 wrote:

Hi
 
I’ve been trying repeatedly to load a sample gff3 file (which I validated at http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online) into webgbrowse but always get
 
“The landmark named NC_004353:1..1000 is not recognized. See the help pages for suggestions.”
 
I’ve attached my gff file.
 
Can you help me?
 
Thanks
 
Mark
 
 



This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. <Galaxy2-[example.3.gff].txt>------------------------------------------------------------------------------
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and get the hardware for free! Learn more.
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Re: landmark not recognized error on valid gff

Mark
<base href="x-msg://63/">

Hi Guys

 

OK, I tried it as in the new attachment and also with

 

NC_004353   .   contig   1   1234567    .    .    .    Name=NC_004353

 

Both give the same error as before

 

Mark

 

From: Podicheti, Ram [mailto:[hidden email]]
Sent: Monday, February 11, 2013 11:02 AM
To: Rose Mark USRE
Cc: <[hidden email]>
Subject: Re: [Gmod-webgbrowse] landmark not recognized error on valid gff

 

Mark,

GBrowse requires the seqID to be defined in the gff3 file as a separate entry. Try entering an additional line in your GFF3 file something like this.

 

NC_004353 .

contig 1 51854

. .

. ID= NC_004353;Name= NC_004353

 

Notice there are 9 columns each separated by a tab. 51854 is the length of the sequence. Let me know if you encounter more issues.

Cheers,

 

Ram

 

On Feb 11, 2013, at 10:31 AM, <[hidden email]>

 wrote:



Hi

 

I’ve been trying repeatedly to load a sample gff3 file (which I validated at http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online) into webgbrowse but always get

 

“The landmark named NC_004353:1..1000 is not recognized. See the help pages for suggestions.”

 

I’ve attached my gff file.

 

Can you help me?

 

Thanks

 

Mark

 

 




This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. <Galaxy2-[example.3.gff].txt>------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013 
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse

 




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Galaxy2-example 3 gff.txt (71K) Download Attachment
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