Query regarding backend MySQL database of Gbrowse

[niharika sharma]

Hello,

I have installed and am using Gbrowse for building an application for our lab. I have installed MySQL and using Gbrowse tutorial have carried out following steps successfully.

C:\Windows> ppm
ppm>   install DBD::mysql
ppm>   quit

% mysql -uroot -p

Enter password: *********

mysql>   create database rice;
Query OK, 1 row affected (0.04 sec)

mysql>   grant all privileges on rice.* to ODBC@localhost;
Query OK, 0 rows affected (0.00 sec)


mysql>   grant select on rice.* to nobody@localhost;
Query OK, 0 rows affected (0.00 sec)

mysql>   quit
Bye

%   bp_seqfeature_load.pl -c -f -d rice rice_all.gff3
loading rice_all.fa...

                                                                                
Building object tree... 0.00s
Loading bulk data into database... 0.00s
load time:  0.02s
loading rice_all.gff3...
                                                                                

Building object tree... 0.00s
Loading bulk data into database... 0.02s

After loading bulk data command it gives an error which I am attaching with

the mail.Kindly go through it and let me know why this error comes and
how I would be able to load the entire data successfully into my

backend database of MySQL.

Awaiting for response.




Regards,


Niharika Sharma.
M.Phil Plant molecular Biology student.

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[Scott Cain-4]

Hello Niharika,

I've only ever seen this reported once before and that was on a
Windows system as well.  Is there any chance that you could either try
the same thing on a Mac or Linux system to see if this is really
Windows specific, or send me or let me know where I can download the
data you are using so I can try it?

Thanks,
Scott


On Mon, Jun 1, 2009 at 5:44 AM, niharika sharma <niharika@...> wrote:

> Hello,
>
> I have installed and am using Gbrowse for building an application for our
> lab. I have installed MySQL and using Gbrowse tutorial have carried out
> following steps successfully.
>
> C:\Windows> ppm
> ppm>   install DBD::mysql
> ppm>   quit
>
> % mysql -uroot -p
>
> Enter password: *********
>
> mysql>   create database rice;
> Query OK, 1 row affected (0.04 sec)
>
> mysql>   grant all privileges on rice.* to ODBC@localhost;
> Query OK, 0 rows affected (0.00 sec)
>
>
> mysql>   grant select on rice.* to nobody@localhost;
> Query OK, 0 rows affected (0.00 sec)
>
> mysql>   quit
> Bye
>
> %   bp_seqfeature_load.pl -c -f -d rice rice_all.gff3
> loading rice_all.fa...
>
>
> Building object tree... 0.00s
> Loading bulk data into database... 0.00s
> load time:  0.02s
> loading rice_all.gff3...
>
>
> Building object tree... 0.00s
> Loading bulk data into database... 0.02s
>
> After loading bulk data command it gives an error which I am attaching with
>
> the mail.Kindly go through it and let me know why this error comes and
> how I would be able to load the entire data successfully into my
>
> backend database of MySQL.
>
> Awaiting for response.
>
>
>
>
> Regards,
>
>
> Niharika Sharma.
> M.Phil Plant molecular Biology student.
>
>
>
> ------------------------------------------------------------------------------
> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> is a gathering of tech-side developers & brand creativity professionals.
> Meet
> the minds behind Google Creative Lab, Visual Complexity, Processing, &
> iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

--
------------------------------------------------------------------------
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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is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
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[ankita narang]

---------- Forwarded message ----------
From: ankita narang <ankita.bioinfo77@...>
Date: Mon, Jun 1, 2009 at 10:20 PM
Subject: Re: [Gmod-gbrowse] Query regarding backend MySQL database of Gbrowse
To: Scott Cain <scott@...>

hi Niharika ,

 

this error comes usually when dont have enough space , do one thing change the data directory in mysql to disk having enough space. actually when we dump the data in windows , it also uses temp folder in windows. I think this can solve  the issue at your end.

 

Ankita

On Mon, Jun 1, 2009 at 8:12 PM, Scott Cain <scott@...> wrote:

Hello Niharika,

I've only ever seen this reported once before and that was on a
Windows system as well.  Is there any chance that you could either try
the same thing on a Mac or Linux system to see if this is really
Windows specific, or send me or let me know where I can download the
data you are using so I can try it?

Thanks,
Scott

On Mon, Jun 1, 2009 at 5:44 AM, niharika sharma <niharika@...> wrote:
> Hello,
>
> I have installed and am using Gbrowse for building an application for our
> lab. I have installed MySQL and using Gbrowse tutorial have carried out
> following steps successfully.
>
> C:\Windows> ppm
> ppm>   install DBD::mysql
> ppm>   quit
>
> % mysql -uroot -p
>
> Enter password: *********
>
> mysql>   create database rice;
> Query OK, 1 row affected (0.04 sec)
>
> mysql>   grant all privileges on rice.* to ODBC@localhost;
> Query OK, 0 rows affected (0.00 sec)
>
>
> mysql>   grant select on rice.* to nobody@localhost;
> Query OK, 0 rows affected (0.00 sec)
>
> mysql>   quit
> Bye
>
> %   bp_seqfeature_load.pl -c -f -d rice rice_all.gff3
> loading rice_all.fa...
>
>
> Building object tree... 0.00s
> Loading bulk data into database... 0.00s
> load time:  0.02s
> loading rice_all.gff3...
>
>
> Building object tree... 0.00s
> Loading bulk data into database... 0.02s
>
> After loading bulk data command it gives an error which I am attaching with
>
> the mail.Kindly go through it and let me know why this error comes and
> how I would be able to load the entire data successfully into my
>
> backend database of MySQL.
>
> Awaiting for response.
>

>
>
>
> Regards,
>
>
> Niharika Sharma.
> M.Phil Plant molecular Biology student.
>
>
>

> ------------------------------------------------------------------------------
> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> is a gathering of tech-side developers & brand creativity professionals.
> Meet
> the minds behind Google Creative Lab, Visual Complexity, Processing, &
> iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



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

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
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is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
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[ankita narang]

---------- Forwarded message ----------
From: ankita narang <ankita.bioinfo77@...>
Date: Tue, Jun 2, 2009 at 3:11 PM
Subject: Re: [Gmod-gbrowse] Query regarding backend MySQL database of Gbrowse
To: niharika sharma <niharika@...>


Hi Niharika,

install mysql admin and there is startupvariables named tab , when u click on tab , there are defined path for 2 directories and u can set path for temp i.e. this one is third directory.

i hope it will help you.

Ankita

On Tue, Jun 2, 2009 at 11:55 AM, niharika sharma <niharika@...> wrote:

Hi Ankita,

Thanx a lot for your suggestion. But please guide me how to change the data directory path of MySQL?

Waiting for your response.

Regards,
Niharika.

On Mon, Jun 1, 2009 at 10:22 PM, ankita narang <ankita.bioinfo77@...> wrote:

---------- Forwarded message ----------
From: ankita narang <ankita.bioinfo77@...>
Date: Mon, Jun 1, 2009 at 10:20 PM
Subject: Re: [Gmod-gbrowse] Query regarding backend MySQL database of Gbrowse
To: Scott Cain <scott@...>

hi Niharika ,

 

this error comes usually when dont have enough space , do one thing change the data directory in mysql to disk having enough space. actually when we dump the data in windows , it also uses temp folder in windows. I think this can solve  the issue at your end.

 

Ankita

On Mon, Jun 1, 2009 at 8:12 PM, Scott Cain <scott@...> wrote:

Hello Niharika,

I've only ever seen this reported once before and that was on a
Windows system as well.  Is there any chance that you could either try
the same thing on a Mac or Linux system to see if this is really
Windows specific, or send me or let me know where I can download the
data you are using so I can try it?

Thanks,
Scott

On Mon, Jun 1, 2009 at 5:44 AM, niharika sharma <niharika@...> wrote:
> Hello,
>
> I have installed and am using Gbrowse for building an application for our
> lab. I have installed MySQL and using Gbrowse tutorial have carried out
> following steps successfully.
>
> C:\Windows> ppm
> ppm>   install DBD::mysql
> ppm>   quit
>
> % mysql -uroot -p
>
> Enter password: *********
>
> mysql>   create database rice;
> Query OK, 1 row affected (0.04 sec)
>
> mysql>   grant all privileges on rice.* to ODBC@localhost;
> Query OK, 0 rows affected (0.00 sec)
>
>
> mysql>   grant select on rice.* to nobody@localhost;
> Query OK, 0 rows affected (0.00 sec)
>
> mysql>   quit
> Bye
>
> %   bp_seqfeature_load.pl -c -f -d rice rice_all.gff3
> loading rice_all.fa...
>
>
> Building object tree... 0.00s
> Loading bulk data into database... 0.00s
> load time:  0.02s
> loading rice_all.gff3...
>
>
> Building object tree... 0.00s
> Loading bulk data into database... 0.02s
>
> After loading bulk data command it gives an error which I am attaching with
>
> the mail.Kindly go through it and let me know why this error comes and
> how I would be able to load the entire data successfully into my
>
> backend database of MySQL.
>
> Awaiting for response.
>

>
>
>
> Regards,
>
>
> Niharika Sharma.
> M.Phil Plant molecular Biology student.
>
>
>

> ------------------------------------------------------------------------------
> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> is a gathering of tech-side developers & brand creativity professionals.
> Meet
> the minds behind Google Creative Lab, Visual Complexity, Processing, &
> iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



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

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
_______________________________________________
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[Scott Cain-4]

Hi Niharika,

I hadn't tried until today; I guessed that this was a Windows specific
problem and was waiting to see if the solutions that Ankita suggested
helped.

Not that it helps much, but it loaded fine on my Linux box.

Scott

On Wed, Jun 10, 2009 at 1:34 AM, niharika sharma<niharika@...> wrote:

> Dear Scott,
>
> Did you see the porblem at your part?
>
> I am waiting to hear from you.
>
> Regards,
> Niharika.
>
> On Tue, Jun 2, 2009 at 11:47 AM, niharika sharma <niharika@...>
> wrote:
>>
>> Dear Scott,
>>
>> I am trying it Mac system also and would also try it using installations
>> done on some other drive than C. Further I am sending you conf file as an
>> attachment and GFF3 file you can download from the link
>>
>> ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.0/all.dir
>> The file name is all.gff3. Please check the error on your part.
>>
>> Hoping to hear from you soon.
>>
>> Regards,
>> Niharika.
>>
>>
>>
>> On Mon, Jun 1, 2009 at 8:12 PM, Scott Cain <scott@...> wrote:
>>>
>>> Hello Niharika,
>>>
>>> I've only ever seen this reported once before and that was on a
>>> Windows system as well.  Is there any chance that you could either try
>>> the same thing on a Mac or Linux system to see if this is really
>>> Windows specific, or send me or let me know where I can download the
>>> data you are using so I can try it?
>>>
>>> Thanks,
>>> Scott
>>>
>>>
>>> On Mon, Jun 1, 2009 at 5:44 AM, niharika sharma <niharika@...>
>>> wrote:
>>> > Hello,
>>> >
>>> > I have installed and am using Gbrowse for building an application for
>>> > our
>>> > lab. I have installed MySQL and using Gbrowse tutorial have carried out
>>> > following steps successfully.
>>> >
>>> > C:\Windows> ppm
>>> > ppm>   install DBD::mysql
>>> > ppm>   quit
>>> >
>>> > % mysql -uroot -p
>>> >
>>> > Enter password: *********
>>> >
>>> > mysql>   create database rice;
>>> > Query OK, 1 row affected (0.04 sec)
>>> >
>>> > mysql>   grant all privileges on rice.* to ODBC@localhost;
>>> > Query OK, 0 rows affected (0.00 sec)
>>> >
>>> >
>>> > mysql>   grant select on rice.* to nobody@localhost;
>>> > Query OK, 0 rows affected (0.00 sec)
>>> >
>>> > mysql>   quit
>>> > Bye
>>> >
>>> > %   bp_seqfeature_load.pl -c -f -d rice rice_all.gff3
>>> > loading rice_all.fa...
>>> >
>>> >
>>> > Building object tree... 0.00s
>>> > Loading bulk data into database... 0.00s
>>> > load time:  0.02s
>>> > loading rice_all.gff3...
>>> >
>>> >
>>> > Building object tree... 0.00s
>>> > Loading bulk data into database... 0.02s
>>> >
>>> > After loading bulk data command it gives an error which I am attaching
>>> > with
>>> >
>>> > the mail.Kindly go through it and let me know why this error comes and
>>> > how I would be able to load the entire data successfully into my
>>> >
>>> > backend database of MySQL.
>>> >
>>> > Awaiting for response.
>>> >
>>> >
>>> >
>>> >
>>> > Regards,
>>> >
>>> >
>>> > Niharika Sharma.
>>> > M.Phil Plant molecular Biology student.
>>> >
>>> >
>>> >
>>> >
>>> > ------------------------------------------------------------------------------
>>> > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
>>> > is a gathering of tech-side developers & brand creativity
>>> > professionals.
>>> > Meet
>>> > the minds behind Google Creative Lab, Visual Complexity, Processing, &
>>> > iPhoneDevCamp as they present alongside digital heavyweights like
>>> > Barbarian
>>> > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
>>> > _______________________________________________
>>> > Gmod-gbrowse mailing list
>>> > Gmod-gbrowse@...
>>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> 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

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