Problems with newly added database

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Problems with newly added database

Hans Vasquez-Gross
Hi All,

    I just added a new gbrowse database using bp_seqfeature_load.  However, when trying to load the page on GBrowse 2.54, I get an error in red saying "Not found".

I loaded this data the same way as our other gbrowse databases which are currently being rendered fine.  I can find the data below in the apache logs.  Would you suggest any other debugging?

[Thu Nov 14 13:34:48 2013] [error] [client 169.237.206.4] Can't find chromosome scaffold194458.3 in default database at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataLoader.pm line 185., referer: http:
[Thu Nov 14 13:34:48 2013] [error] [client 169.237.206.4] Can't find chromosome scaffold866094 in default database at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataLoader.pm line 185., referer: http:/
[Thu Nov 14 13:34:48 2013] [error] [client 169.237.206.4] Can't find chromosome tscaffold4714 in default database at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataLoader.pm line 185., referer: http://
[Thu Nov 14 13:34:48 2013] [error] [client 169.237.206.4] Can't find chromosome C32158012 in default database at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataLoader.pm line 185., referer: http:/
[Thu Nov 14 13:34:48 2013] [error] [client 169.237.206.4] Can't find chromosome C32534940 in default database at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/DataLoader.pm line 185., referer: http://

Thank you,
-Hans

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Re: Problems with newly added database

Scott Cain
Hi Hans,

Is there a gff line that defines what scaffold194458.3 is?  That is almost always the problem.

Scott



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On Nov 14, 2013, at 5:04 PM, Hans Vasquez-Gross <[hidden email]> wrote:

> scaffold194458.3

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Re: Problems with newly added database

Hans Vasquez-Gross
Hi Scott,

The definition for that scaffold is below.  I tested to make sure my db configuration was functioning by changing it to another functioning gbrowse database.  The exon data got rendered and displayed properly, so I think it's an issue with the gff3 or when loading the initial gff3 data into the database.  The gff3 validates fine when running it through a validator.  I'm currently re-loading a new database with this same gff3 data.

scaffold194458.3        maker   gene    39781   40633   .       -       .       ID=maker-jcf7180062625729-snap-gene-0.2;Name=maker-jcf7180062625729-snap-gene-0.2;Dbxref=Gene3D:G3DSA:1.10.238.10,InterPro:IPR002048,InterPro:IPR011992,InterPro:IPR018247,InterPro:IPR018248,InterPro:IPR018249,PANTHER:PTHR10891,PANTHER:PTHR10891:SF41,Pfam:PF00036,Prosite:PS00018,Prosite:PS50222,SMART:SM00054,superfamily:SSF47473;Ontology_term=GO:0005509;
scaffold194458.3        maker   mRNA    39781   40633   .       -       .       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1;Parent=maker-jcf7180062625729-snap-gene-0.2;Name=maker-jcf7180062625729-snap-gene-0.2-mRNA-1;_AED=0.20;_eAED=0.29;_QI=7|0|0|1|0|0|2|0|159;Dbxref=Gene3D:G3DSA:1.10.238.10,InterPro:IPR002048,InterPro:IPR011992,InterPro:IPR018247,InterPro:IPR018248,InterPro:IPR018249,PANTHER:PTHR10891,PANTHER:PTHR10891:SF41,Pfam:PF00036,Prosite:PS00018,Prosite:PS50222,SMART:SM00054,superfamily:SSF47473;Ontology_term=GO:0005509;
scaffold194458.3        maker   exon    40452   40633   .       -       .       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1:exon:45;Parent=maker-jcf7180062625729-snap-gene-0.2-mRNA-1
scaffold194458.3        maker   exon    39781   40082   .       -       .       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1:exon:44;Parent=maker-jcf7180062625729-snap-gene-0.2-mRNA-1
scaffold194458.3        maker   five_prime_UTR  40627   40633   .       -       .       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1:five_prime_utr;Parent=maker-jcf7180062625729-snap-gene-0.2-mRNA-1
scaffold194458.3        maker   CDS     40452   40626   .       -       0       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1:cds;Parent=maker-jcf7180062625729-snap-gene-0.2-mRNA-1
scaffold194458.3        maker   CDS     39781   40082   .       -       2       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1:cds;Parent=maker-jcf7180062625729-snap-gene-0.2-mRNA-1


Thank you,
-Hans


On Thu, Nov 14, 2013 at 4:12 PM, Scott Cain <[hidden email]> wrote:
Hi Hans,

Is there a gff line that defines what scaffold194458.3 is?  That is almost always the problem.

Scott



Sent from my iPad

On Nov 14, 2013, at 5:04 PM, Hans Vasquez-Gross <[hidden email]> wrote:

> scaffold194458.3



--
Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Phone: (530) 752-0609
Skype: hansvg.ucd

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Re: Problems with newly added database

Scott Cain
Hi Hans,

I disagree; you sent gff that defines a gene and it's parts.  There's not a line that has scaffold in the type position (third column).

Scott



Sent from my iPad

On Nov 14, 2013, at 7:24 PM, Hans Vasquez-Gross <[hidden email]> wrote:

Hi Scott,

The definition for that scaffold is below.  I tested to make sure my db configuration was functioning by changing it to another functioning gbrowse database.  The exon data got rendered and displayed properly, so I think it's an issue with the gff3 or when loading the initial gff3 data into the database.  The gff3 validates fine when running it through a validator.  I'm currently re-loading a new database with this same gff3 data.

scaffold194458.3        maker   gene    39781   40633   .       -       .       ID=maker-jcf7180062625729-snap-gene-0.2;Name=maker-jcf7180062625729-snap-gene-0.2;Dbxref=Gene3D:G3DSA:1.10.238.10,InterPro:IPR002048,InterPro:IPR011992,InterPro:IPR018247,InterPro:IPR018248,InterPro:IPR018249,PANTHER:PTHR10891,PANTHER:PTHR10891:SF41,Pfam:PF00036,Prosite:PS00018,Prosite:PS50222,SMART:SM00054,superfamily:SSF47473;Ontology_term=GO:0005509;
scaffold194458.3        maker   mRNA    39781   40633   .       -       .       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1;Parent=maker-jcf7180062625729-snap-gene-0.2;Name=maker-jcf7180062625729-snap-gene-0.2-mRNA-1;_AED=0.20;_eAED=0.29;_QI=7|0|0|1|0|0|2|0|159;Dbxref=Gene3D:G3DSA:1.10.238.10,InterPro:IPR002048,InterPro:IPR011992,InterPro:IPR018247,InterPro:IPR018248,InterPro:IPR018249,PANTHER:PTHR10891,PANTHER:PTHR10891:SF41,Pfam:PF00036,Prosite:PS00018,Prosite:PS50222,SMART:SM00054,superfamily:SSF47473;Ontology_term=GO:0005509;
scaffold194458.3        maker   exon    40452   40633   .       -       .       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1:exon:45;Parent=maker-jcf7180062625729-snap-gene-0.2-mRNA-1
scaffold194458.3        maker   exon    39781   40082   .       -       .       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1:exon:44;Parent=maker-jcf7180062625729-snap-gene-0.2-mRNA-1
scaffold194458.3        maker   five_prime_UTR  40627   40633   .       -       .       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1:five_prime_utr;Parent=maker-jcf7180062625729-snap-gene-0.2-mRNA-1
scaffold194458.3        maker   CDS     40452   40626   .       -       0       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1:cds;Parent=maker-jcf7180062625729-snap-gene-0.2-mRNA-1
scaffold194458.3        maker   CDS     39781   40082   .       -       2       ID=maker-jcf7180062625729-snap-gene-0.2-mRNA-1:cds;Parent=maker-jcf7180062625729-snap-gene-0.2-mRNA-1


Thank you,
-Hans


On Thu, Nov 14, 2013 at 4:12 PM, Scott Cain <[hidden email]> wrote:
Hi Hans,

Is there a gff line that defines what scaffold194458.3 is?  That is almost always the problem.

Scott



Sent from my iPad

On Nov 14, 2013, at 5:04 PM, Hans Vasquez-Gross <[hidden email]> wrote:

> scaffold194458.3



--
Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Phone: (530) 752-0609
Skype: hansvg.ucd

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