[Gmod-gbrowse] GMOD gives : "not found" error

[Scott Cain]

Hi Seyed,

Please always cc the gbrowse mailing list (as I've done here).

The GBrowse "not found" message is usually the result of a problem with the
GFF, and that problem is usually not having defined the reference sequence
in the GFF. In your example, you're looking for a reference sequence
called chr20. Is there a line in your GFF that looks something like:

chr20 . chromosome 1 1243456788 . . . Name=chr20

where the big number is the length of the feature? The important bit is
that the Name attribute match the name in the first column.

Scott


On Tue, Jun 7, 2016 at 7:24 AM, Seyed Ahmad Mousavi <

Dear Dr. Cain,
I've install last version of GMOD in Ubuntu 16.04 , it works nicely for
sample and template but when I wanted to run GMOD on Chr2 and Chr20 (using
http://gmod.org/wiki/GBrowse_NGS_Tutorial#Displaying_Human_Data_in_GBrowse
Inserting fasta and gff file by *bp_seqfeature_load.pl
<http://bp_seqfeature_load.pl>* tool has done correctly.
*[annotations:database] db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql -dsn human
-user www-data -pass pass1*
But I got *"Not found" red error* at the top of the page, I could not
found any thing in apache2 error_log.
You can see error page of GMOD at browser below image.
How can I fix this problem?
Kind regards,
Ahmad

[Scott Cain]

Hi Ahmad,

Like I wrote in my previous email, you need a line in your GFF that
identifies chr20 (and any other reference sequences you have), like this:

chr20 . chromosome 1 12345678 . . . Name=chr20

You don't have to reload your database with all of the mRNA data, just
create a file with these lines in them and load them into the same database.

Scott


On Sat, Jun 11, 2016 at 6:44 AM, Seyed Ahmad Mousavi <

Dear Dr. Cain,
Thanks for reply and answering the problem.
Yes you are right there is no Name column which equal to chr20, instead it
includes Gene name, Ensemble Id or ... for Name field.
*How can I fix that file in the right way?*
*http://www.compbio.ox.ac.uk/data/HUMAN_HG18/ensembl/chr20_ens_annots.gff
<http://www.compbio.ox.ac.uk/data/HUMAN_HG18/ensembl/chr20_ens_annots.gff>*
chr20 Ensembl mRNA 54794444 54794550 . - .
ID=ENSG00000207158;Name=ENSG00000207158;description=ENSG00000207158;ensgene_id=ENSG00000207158
chr20 Ensembl exon 54794444 54794550 . - .
ID=ENSE00001499437;Parent=ENSG00000207158
chr20 Ensembl mRNA 32612007 32728750 . - . ID=PIGU;Name=PIGU;description=GPI
transamidase component PIG-U (Phosphatidylinositol-glycan biosynthesis
class U protein) (Cell division cycle protein 91-like 1) (CDC91-like 1
protein).;ensgene_id=ENSG00000101464
chr20 Ensembl exon 32612007 32612444 . - . ID=ENSE00001414279;Parent=PIGU
chr20 Ensembl exon 32626569 32626711 . - . ID=ENSE00000860124;Parent=PIGU
Kind regards,
Ahmad

Post by Scott Cain
Hi Seyed,
Please always cc the gbrowse mailing list (as I've done here).
The GBrowse "not found" message is usually the result of a problem with
the GFF, and that problem is usually not having defined the reference
sequence in the GFF. In your example, you're looking for a reference
sequence called chr20. Is there a line in your GFF that looks something
chr20 . chromosome 1 1243456788 . . . Name=chr20
where the big number is the length of the feature? The important bit is
that the Name attribute match the name in the first column.
Scott
On Tue, Jun 7, 2016 at 7:24 AM, Seyed Ahmad Mousavi <

Dear Dr. Cain,
I've install last version of GMOD in Ubuntu 16.04 , it works nicely for
sample and template but when I wanted to run GMOD on Chr2 and Chr20 (using
http://gmod.org/wiki/GBrowse_NGS_Tutorial#Displaying_Human_Data_in_GBrowse
Inserting fasta and gff file by *bp_seqfeature_load.pl
<http://bp_seqfeature_load.pl>* tool has done correctly.
*[annotations:database] db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql -dsn human
-user www-data -pass pass1*
But I got *"Not found" red error* at the top of the page, I could not
found any thing in apache2 error_log.
You can see error page of GMOD at browser below image.
How can I fix this problem?
Kind regards,
Ahmad

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

[Seyed Ahmad Mousavi]

Dear Dr. Cain,

Many thanks for reply, it just worked.
I added the line to the beginning of my GFF file then inserting them to
Mysql.


Many thanks,
Ahmad

Post by Scott Cain
Hi Ahmad,
Like I wrote in my previous email, you need a line in your GFF that
chr20 . chromosome 1 12345678 . . . Name=chr20
You don't have to reload your database with all of the mRNA data, just
create a file with these lines in them and load them into the same database.
Scott
On Sat, Jun 11, 2016 at 6:44 AM, Seyed Ahmad Mousavi <

Dear Dr. Cain,
Thanks for reply and answering the problem.
Yes you are right there is no Name column which equal to chr20, instead
it includes Gene name, Ensemble Id or ... for Name field.
*How can I fix that file in the right way?*
*http://www.compbio.ox.ac.uk/data/HUMAN_HG18/ensembl/chr20_ens_annots.gff
<http://www.compbio.ox.ac.uk/data/HUMAN_HG18/ensembl/chr20_ens_annots.gff>*
chr20 Ensembl mRNA 54794444 54794550 . - .
ID=ENSG00000207158;Name=ENSG00000207158;description=ENSG00000207158;ensgene_id=ENSG00000207158
chr20 Ensembl exon 54794444 54794550 . - .
ID=ENSE00001499437;Parent=ENSG00000207158
chr20 Ensembl mRNA 32612007 32728750 . - . ID=PIGU;Name=PIGU;description=GPI
transamidase component PIG-U (Phosphatidylinositol-glycan biosynthesis
class U protein) (Cell division cycle protein 91-like 1) (CDC91-like 1
protein).;ensgene_id=ENSG00000101464
chr20 Ensembl exon 32612007 32612444 . - . ID=ENSE00001414279;Parent=PIGU
chr20 Ensembl exon 32626569 32626711 . - . ID=ENSE00000860124;Parent=PIGU
Kind regards,
Ahmad

Post by Scott Cain
Hi Seyed,
Please always cc the gbrowse mailing list (as I've done here).
The GBrowse "not found" message is usually the result of a problem with
the GFF, and that problem is usually not having defined the reference
sequence in the GFF. In your example, you're looking for a reference
sequence called chr20. Is there a line in your GFF that looks something
chr20 . chromosome 1 1243456788 . . . Name=chr20
where the big number is the length of the feature? The important bit is
that the Name attribute match the name in the first column.
Scott
On Tue, Jun 7, 2016 at 7:24 AM, Seyed Ahmad Mousavi <

Dear Dr. Cain,
I've install last version of GMOD in Ubuntu 16.04 , it works nicely for
sample and template but when I wanted to run GMOD on Chr2 and Chr20 (using
http://gmod.org/wiki/GBrowse_NGS_Tutorial#Displaying_Human_Data_in_GBrowse
Inserting fasta and gff file by *bp_seqfeature_load.pl
<http://bp_seqfeature_load.pl>* tool has done correctly.
*[annotations:database] db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql -dsn human
-user www-data -pass pass1*
But I got *"Not found" red error* at the top of the page, I could not
found any thing in apache2 error_log.
You can see error page of GMOD at browser below image.
How can I fix this problem?
Kind regards,
Ahmad

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

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