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Re: GMOD gives : "not found" error

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Scott Cain

Re: GMOD gives : "not found" error

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 <[hidden email]> wrote:

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 Mysql) based on following tutorial :

http://gmod.org/wiki/GBrowse_NGS_Tutorial#Displaying_Human_Data_in_GBrowse

Inserting fasta and gff file by bp_seqfeature_load.pl tool has done correctly.
I gave all privilages to www-data in mysql and in human.conf I changed :

[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

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Seyed Ahmad Mousavi

Re: GMOD gives : "not found" error

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?

Please take a look at below chr_20.gff file :

http://www.compbio.ox.ac.uk/data/HUMAN_HG18/ensembl/chr20_ens_annots.gff

You can see also number if GFF lines:

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

On Sat, Jun 11, 2016 at 12:40 AM, Scott Cain <[hidden email]> wrote:

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 <[hidden email]> wrote:
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 Mysql) based on following tutorial :

http://gmod.org/wiki/GBrowse_NGS_Tutorial#Displaying_Human_Data_in_GBrowse

Inserting fasta and gff file by bp_seqfeature_load.pl tool has done correctly.
I gave all privilages to www-data in mysql and in human.conf I changed :

[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

Re: GMOD gives : "not found" error

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 <[hidden email]> wrote:

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?

Please take a look at below chr_20.gff file :

http://www.compbio.ox.ac.uk/data/HUMAN_HG18/ensembl/chr20_ens_annots.gff

You can see also number if GFF lines:

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

On Sat, Jun 11, 2016 at 12:40 AM, Scott Cain <[hidden email]> wrote:
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 <[hidden email]> wrote:
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 Mysql) based on following tutorial :

http://gmod.org/wiki/GBrowse_NGS_Tutorial#Displaying_Human_Data_in_GBrowse

Inserting fasta and gff file by bp_seqfeature_load.pl tool has done correctly.
I gave all privilages to www-data in mysql and in human.conf I changed :

[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/) <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

Seyed Ahmad Mousavi

Re: GMOD gives : "not found" error

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

On Sat, Jun 11, 2016 at 6:19 PM, Scott Cain <[hidden email]> wrote:

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 <[hidden email]> wrote:
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?

Please take a look at below chr_20.gff file :

http://www.compbio.ox.ac.uk/data/HUMAN_HG18/ensembl/chr20_ens_annots.gff

You can see also number if GFF lines:

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

On Sat, Jun 11, 2016 at 12:40 AM, Scott Cain <[hidden email]> wrote:
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 <[hidden email]> wrote:
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 Mysql) based on following tutorial :

http://gmod.org/wiki/GBrowse_NGS_Tutorial#Displaying_Human_Data_in_GBrowse

Inserting fasta and gff file by bp_seqfeature_load.pl tool has done correctly.
I gave all privilages to www-data in mysql and in human.conf I changed :

[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/)    <a href="tel:216-392-3087" value="+12163923087" target="_blank">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