error running load_seqdatabase.pl

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error running load_seqdatabase.pl

Angshu Kar
Hi,

I'm getting the following error while trying to run :

./load_seqdatabase.pl -host localhost -dbname USBA -dbuser postgres -format
genbank NC_003076.gbk

Loading NC_003076.gbk ...

------------- EXCEPTION  -------------
MSG: failed to open connection: Can't connect to local MySQL server through
socket '/var/lib/mysql/mysql.sock' (2)
STACK Bio::DB::DBI::base::new_connection /home/akar/local/perl/Bio/DB/D
BI/base.pm:255
STACK Bio::DB::DBI::base::get_connection /home/akar/local/perl/Bio/DB/D
BI/base.pm:215
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh
/home/akar/local/perl/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1477
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::rollback
/home/akar/local/perl/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1396
STACK toplevel ./load_seqdatabase.pl:627

But I've a postgreSQL db and not a MySQL one...could anyone please guide me
troubleshoot this?

Thanks,
Angshu

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Re: error running load_seqdatabase.pl

Sean Davis-3

----- Original Message -----
From: "Angshu Kar" <[hidden email]>
To: "bioperl-l" <[hidden email]>
Sent: Thursday, December 29, 2005 5:50 PM
Subject: [Bioperl-l] error running load_seqdatabase.pl


> Hi,
>
> I'm getting the following error while trying to run :
>
> ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
> postgres -format
> genbank NC_003076.gbk
>
> But I've a postgreSQL db and not a MySQL one...could anyone please guide
> me
> troubleshoot this?

Angshu,

I would probably start with:

perldoc load_seqdatabase.pl

I think that will likely give you your answer.  Again, it is best to exhaust
the resources at hand and to let the list know that you have done so
(like--"I read the perldoc and tried this....").

Sean


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Re: error running load_seqdatabase.pl

Torsten Seemann
In reply to this post by Angshu Kar
> I'm getting the following error while trying to run :
> ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser postgres -format
> genbank NC_003076.gbk
> MSG: failed to open connection: Can't connect to local MySQL server through
> socket '/var/lib/mysql/mysql.sock' (2)
> But I've a postgreSQL db and not a MySQL one...could anyone please guide me
> troubleshoot this?

Did you read the documentation for the load_seqdatabase.pl script?

It's in the script itself!

    =item --driver $driver
    the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle [mysql]

The default DBI driver is [mysql].

I think you want the option "-driver Pg".

--
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/
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Re: error running load_seqdatabase.pl

Hilmar Lapp
BTW since Sep 1 there is no default for the driver anymore in the
script nor in Bio::DB::BioDB->new() (which you'd use to instantiate a
$db handle in your own script). Deeper inside there is still an
implementation module (Bio::DB::SimpleDBContext) that sets mysql as the
default driver if neither driver nor dsn are provided.

I.e., what I'm saying is don't rely anymore on mysql being the default
driver as this behavior may go away at any time - always specify it
explicitly.

On another note, if you're always connecting to the same biosql
instance, you may want to put a file .bioperldb in your home directory
and use option --initrc. See the POD.

        -hilmar

On Dec 29, 2005, at 5:26 PM, Torsten Seemann wrote:

>> I'm getting the following error while trying to run :
>> ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser postgres
>> -format
>> genbank NC_003076.gbk
>> MSG: failed to open connection: Can't connect to local MySQL server
>> through
>> socket '/var/lib/mysql/mysql.sock' (2)
>> But I've a postgreSQL db and not a MySQL one...could anyone please
>> guide me
>> troubleshoot this?
>
> Did you read the documentation for the load_seqdatabase.pl script?
>
> It's in the script itself!
>
>    =item --driver $driver
>    the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle [mysql]
>
> The default DBI driver is [mysql].
>
> I think you want the option "-driver Pg".
>
> --
> Torsten Seemann
> Victorian Bioinformatics Consortium, Monash University, Australia
> http://www.vicbioinformatics.com/
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


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Re: error running load_seqdatabase.pl

Angshu Kar
In reply to this post by Torsten Seemann
I'm sorry that I missed it! Thanks for pointing it out.
Also thanks Hilmar for the update.

Angshu

On 12/29/05, Torsten Seemann <[hidden email] >
wrote:

>
> > I'm getting the following error while trying to run :
> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser postgres
> -format
> > genbank NC_003076.gbk
> > MSG: failed to open connection: Can't connect to local MySQL server
> through
> > socket '/var/lib/mysql/mysql.sock' (2)
> > But I've a postgreSQL db and not a MySQL one...could anyone please guide
> me
> > troubleshoot this?
>
> Did you read the documentation for the load_seqdatabase.pl script?
>
> It's in the script itself!
>
>     =item --driver $driver
>     the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle [mysql]
>
> The default DBI driver is [mysql].
>
> I think you want the option "-driver Pg".
>
> --
> Torsten Seemann
> Victorian Bioinformatics Consortium, Monash University, Australia
> http://www.vicbioinformatics.com/
>

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Re: error running load_seqdatabase.pl

Angshu Kar
Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl --dbname=USBA
--dbuser=postgres --format=genbank  --driver=Pg --debug  NC_003076.gbk)
 is getting killed after the follwoing step?

Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer for
Bio::DB::BioSQL::BiosequenceAdaptor
preparing SELECT statement: SELECT bioentry_id FROM biosequence WHERE
bioentry_id = ?

Killed

I'm using a linux box. This didn't happen for a different i/p file!

Thanks,
Angshu


On 12/29/05, Angshu Kar <[hidden email]> wrote:

>
> I'm sorry that I missed it! Thanks for pointing it out.
> Also thanks Hilmar for the update.
>
> Angshu
>
> On 12/29/05, Torsten Seemann < [hidden email] >
> wrote:
> >
> > > I'm getting the following error while trying to run :
> > > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser postgres
> > -format
> > > genbank NC_003076.gbk
> > > MSG: failed to open connection: Can't connect to local MySQL server
> > through
> > > socket '/var/lib/mysql/mysql.sock' (2)
> > > But I've a postgreSQL db and not a MySQL one...could anyone please
> > guide me
> > > troubleshoot this?
> >
> > Did you read the documentation for the load_seqdatabase.pl script?
> >
> > It's in the script itself!
> >
> >     =item --driver $driver
> >     the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle [mysql]
> >
> >
> > The default DBI driver is [mysql].
> >
> > I think you want the option "-driver Pg".
> >
> > --
> > Torsten Seemann
> > Victorian Bioinformatics Consortium, Monash University, Australia
> > http://www.vicbioinformatics.com/
> >
>
>

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Re: error running load_seqdatabase.pl

Angshu Kar
Also how to run the bioperl-db test ? I mean do I have to reinstall it to
run the make test command?



On 12/30/05, Angshu Kar <[hidden email]> wrote:

>
> Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl --dbname=USBA
> --dbuser=postgres --format=genbank  --driver=Pg --debug  NC_003076.gbk)
>  is getting killed after the follwoing step?
>
> Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer for
> Bio::DB::BioSQL::BiosequenceAdaptor
> preparing SELECT statement: SELECT bioentry_id FROM biosequence WHERE
> bioentry_id = ?
>
> Killed
>
> I'm using a linux box. This didn't happen for a different i/p file!
>
> Thanks,
> Angshu
>
>
> On 12/29/05, Angshu Kar <[hidden email]> wrote:
> >
> > I'm sorry that I missed it! Thanks for pointing it out.
> > Also thanks Hilmar for the update.
> >
> > Angshu
> >
> > On 12/29/05, Torsten Seemann < [hidden email] >
> > wrote:
> > >
> > > > I'm getting the following error while trying to run :
> > > > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser postgres
> > > -format
> > > > genbank NC_003076.gbk
> > > > MSG: failed to open connection: Can't connect to local MySQL server
> > > through
> > > > socket '/var/lib/mysql/mysql.sock' (2)
> > > > But I've a postgreSQL db and not a MySQL one...could anyone please
> > > guide me
> > > > troubleshoot this?
> > >
> > > Did you read the documentation for the load_seqdatabase.pl script?
> > >
> > > It's in the script itself!
> > >
> > >     =item --driver $driver
> > >     the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
> > > [mysql]
> > >
> > > The default DBI driver is [mysql].
> > >
> > > I think you want the option "-driver Pg".
> > >
> > > --
> > > Torsten Seemann
> > > Victorian Bioinformatics Consortium, Monash University, Australia
> > > http://www.vicbioinformatics.com/
> > >
> >
> >
>

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Re: error running load_seqdatabase.pl

Hilmar Lapp
In reply to this post by Angshu Kar
If it didn't happen for a different input file, can you tell what is
special about this one? The file name lets me guess the input is a
contig or even a full chromosome? Is the input on which the process
wasn't killed of the same nature? Are the sequences of comparable or
vastly different lengths? Is there only a single contig in the
offending input? Can you reproduce the problem on an empty database
with input containing a single entry? If so, let me know where I can
get that file from and I'll try to reproduce it locally.

        -hilmar

On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:

> Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
> --dbname=USBA --dbuser=postgres --format=genbank  --driver=Pg --debug 
> NC_003076.gbk)
>  is getting killed after the follwoing step?
>
>  Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer
> for Bio::DB::BioSQL::BiosequenceAdaptor
> preparing SELECT statement: SELECT bioentry_id FROM biosequence WHERE
> bioentry_id = ?
>
> Killed
>
> I'm using a linux box. This didn't happen for a different i/p file!
>
> Thanks,
> Angshu
>
>
> On 12/29/05, Angshu Kar <[hidden email]> wrote: I'm sorry that I
> missed it! Thanks for pointing it out.
>> Also thanks Hilmar for the update.
>>
>> Angshu
>>
>>
>> On 12/29/05, Torsten Seemann < [hidden email]
>> > wrote:> I'm getting the following error while trying to run :
>>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
>>> postgres -format
>>> > genbank NC_003076.gbk
>>> > MSG: failed to open connection: Can't connect to local MySQL
>>> server through
>>> > socket '/var/lib/mysql/mysql.sock' (2)
>>> > But I've a postgreSQL db and not a MySQL one...could anyone please
>>> guide me
>>> > troubleshoot this?
>>>
>>> Did you read the documentation for the load_seqdatabase.pl script?
>>>
>>> It's in the script itself!
>>>
>>>     =item --driver $driver
>>>     the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
>>> [mysql]
>>>
>>> The default DBI driver is [mysql].
>>>
>>> I think you want the option "-driver Pg".
>>>
>>> --
>>> Torsten Seemann
>>> Victorian Bioinformatics Consortium, Monash University, Australia
>>>  http://www.vicbioinformatics.com/
>>
>>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



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Re: error running load_seqdatabase.pl

Hilmar Lapp
In reply to this post by Angshu Kar
No. Just in the base directory of your unpacked bioperl-db download
type 'make test' (obviously without the quotes).

If you installed bioperl in a non-standard place make sure you set the
PERL5LIB environment appropriately before doing this.

        -hilmar

On Dec 30, 2005, at 2:36 PM, Angshu Kar wrote:

> Also how to run the bioperl-db test ? I mean do I have to reinstall it
> to run the make test command?
>
>
>
> On 12/30/05, Angshu Kar < [hidden email]> wrote:Any clues why my
> load_seqdatabase.pl (./load_seqdatabase.pl --dbname=USBA
> --dbuser=postgres --format=genbank  --driver=Pg --debug 
> NC_003076.gbk)
>>  is getting killed after the follwoing step?
>>
>>  Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer
>> for Bio::DB::BioSQL::BiosequenceAdaptor
>> preparing SELECT statement: SELECT bioentry_id FROM biosequence WHERE
>> bioentry_id = ?
>>
>> Killed
>>
>> I'm using a linux box. This didn't happen for a different i/p file!
>>
>> Thanks,
>> Angshu
>>
>>
>> On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm sorry that I
>> missed it! Thanks for pointing it out.
>>> Also thanks Hilmar for the update.
>>>
>>> Angshu
>>>
>>>
>>> On 12/29/05, Torsten Seemann <
>>> [hidden email] > wrote:> I'm getting the
>>> following error while trying to run :
>>>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
>>>> postgres -format
>>>> > genbank NC_003076.gbk
>>>> > MSG: failed to open connection: Can't connect to local MySQL
>>>> server through
>>>> > socket '/var/lib/mysql/mysql.sock' (2)
>>>> > But I've a postgreSQL db and not a MySQL one...could anyone
>>>> please guide me
>>>> > troubleshoot this?
>>>>
>>>> Did you read the documentation for the load_seqdatabase.pl script?
>>>>
>>>> It's in the script itself!
>>>>
>>>>     =item --driver $driver
>>>>     the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
>>>> [mysql]
>>>>
>>>> The default DBI driver is [mysql].
>>>>
>>>> I think you want the option "-driver Pg".
>>>>
>>>> --
>>>> Torsten Seemann
>>>> Victorian Bioinformatics Consortium, Monash University, Australia
>>>>  http://www.vicbioinformatics.com/
>>>
>>
>>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



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Re: error running load_seqdatabase.pl

Angshu Kar
In reply to this post by Hilmar Lapp
Yes Hilmar its indeed a full sequence of chromosome. I got it from
ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
I tried with the .faa and .fna files and they ran successfully.
Also I missed a line (may be relevant) in the debug o/p:
no adaptor found for class Bio::Annotation::TypeManager

Thanks,
Angshu


On 12/30/05, Hilmar Lapp <[hidden email]> wrote:

>
> If it didn't happen for a different input file, can you tell what is
> special about this one? The file name lets me guess the input is a
> contig or even a full chromosome? Is the input on which the process
> wasn't killed of the same nature? Are the sequences of comparable or
> vastly different lengths? Is there only a single contig in the
> offending input? Can you reproduce the problem on an empty database
> with input containing a single entry? If so, let me know where I can
> get that file from and I'll try to reproduce it locally.
>
>         -hilmar
>
> On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:
>
> > Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
> > --dbname=USBA --dbuser=postgres --format=genbank --driver=Pg --debug
> > NC_003076.gbk)
> > is getting killed after the follwoing step?
> >
> >  Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer
> > for Bio::DB::BioSQL::BiosequenceAdaptor
> > preparing SELECT statement: SELECT bioentry_id FROM biosequence WHERE
> > bioentry_id = ?
> >
> > Killed
> >
> > I'm using a linux box. This didn't happen for a different i/p file!
> >
> > Thanks,
> > Angshu
> >
> >
> > On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm sorry that I
> > missed it! Thanks for pointing it out.
> >> Also thanks Hilmar for the update.
> >>
> >> Angshu
> >>
> >>
> >> On 12/29/05, Torsten Seemann < [hidden email]
> >> > wrote:> I'm getting the following error while trying to run :
> >>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
> >>> postgres -format
> >>> > genbank NC_003076.gbk
> >>> > MSG: failed to open connection: Can't connect to local MySQL
> >>> server through
> >>> > socket '/var/lib/mysql/mysql.sock' (2)
> >>> > But I've a postgreSQL db and not a MySQL one...could anyone please
> >>> guide me
> >>> > troubleshoot this?
> >>>
> >>> Did you read the documentation for the load_seqdatabase.pl script?
> >>>
> >>> It's in the script itself!
> >>>
> >>> =item --driver $driver
> >>> the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
> >>> [mysql]
> >>>
> >>> The default DBI driver is [mysql].
> >>>
> >>> I think you want the option "-driver Pg".
> >>>
> >>> --
> >>> Torsten Seemann
> >>> Victorian Bioinformatics Consortium, Monash University, Australia
> >>>  http://www.vicbioinformatics.com/
> >>
> >>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>

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Re: error running load_seqdatabase.pl

Hilmar Lapp
Did you empty the database after the previous runs?

Also, you haven't reported your hw setup. In particular, how much
memory and swap do you have, is Pg running locally (your command line
suggests it does), and how much memory have you allocated to Pg?

        -hilmar

On Dec 30, 2005, at 3:01 PM, Angshu Kar wrote:

> Yes Hilmar its indeed a full sequence of chromosome. I got it from
> ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
> I tried with the .faa and .fna files and they ran successfully.
> Also I missed a line (may be relevant) in the debug o/p:
> no adaptor found for class Bio::Annotation::TypeManager
>
> Thanks,
> Angshu
>
>
> On 12/30/05, Hilmar Lapp < [hidden email]> wrote:
>> special about this one? The file name lets me guess the input is a
>> contig or even a full chromosome? Is the input on which the process
>> wasn't killed of the same nature? Are the sequences of comparable or
>> vastly different lengths? Is there only a single contig in the
>> offending input? Can you reproduce the problem on an empty database
>> with input containing a single entry? If so, let me know where I can
>> get that file from and I'll try to reproduce it locally.
>>
>>         -hilmar
>>
>> On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:
>>
>> > Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
>> > --dbname=USBA --dbuser=postgres --format=genbank --driver=Pg --debug
>> > NC_003076.gbk)
>> > is getting killed after the follwoing step?
>> >
>> >  Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer
>> > for Bio::DB::BioSQL::BiosequenceAdaptor
>> > preparing SELECT statement: SELECT bioentry_id FROM biosequence
>> WHERE
>> > bioentry_id = ?
>> >
>> > Killed
>> >
>> > I'm using a linux box. This didn't happen for a different i/p file!
>> >
>> > Thanks,
>> > Angshu
>> >
>> >
>> > On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm sorry that
>> I
>> > missed it! Thanks for pointing it out.
>> >> Also thanks Hilmar for the update.
>> >>
>> >> Angshu
>> >>
>> >>
>> >> On 12/29/05, Torsten Seemann <
>> [hidden email]
>> >> > wrote:> I'm getting the following error while trying to run :
>> >>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
>> >>> postgres -format
>> >>> > genbank NC_003076.gbk
>> >>> > MSG: failed to open connection: Can't connect to local MySQL
>> >>> server through
>> >>> > socket '/var/lib/mysql/mysql.sock' (2)
>> >>> > But I've a postgreSQL db and not a MySQL one...could anyone
>> please
>> >>> guide me
>> >>> > troubleshoot this?
>> >>>
>> >>> Did you read the documentation for the load_seqdatabase.pl script?
>> >>>
>> >>> It's in the script itself!
>> >>>
>> >>> =item --driver $driver
>> >>> the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
>> >>> [mysql]
>> >>>
>> >>> The default DBI driver is [mysql].
>> >>>
>> >>> I think you want the option "-driver Pg".
>> >>>
>>  >>> --
>> >>> Torsten Seemann
>> >>> Victorian Bioinformatics Consortium, Monash University, Australia
>> >>>   http://www.vicbioinformatics.com/
>> >>
>> >>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



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Re: error running load_seqdatabase.pl

Angshu Kar
I've no clue about my Pg setup! It has been done by the sysadmin! :(
Could you please tell me the commands and I can run and let you know the
reports?

thanks,
angshu

On 12/30/05, Hilmar Lapp <[hidden email]> wrote:

>
> Did you empty the database after the previous runs?
>
> Also, you haven't reported your hw setup. In particular, how much
> memory and swap do you have, is Pg running locally (your command line
> suggests it does), and how much memory have you allocated to Pg?
>
>         -hilmar
>
> On Dec 30, 2005, at 3:01 PM, Angshu Kar wrote:
>
> > Yes Hilmar its indeed a full sequence of chromosome. I got it from
> > ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
> > I tried with the .faa and .fna files and they ran successfully.
> > Also I missed a line (may be relevant) in the debug o/p:
> > no adaptor found for class Bio::Annotation::TypeManager
> >
> > Thanks,
> > Angshu
> >
> >
> > On 12/30/05, Hilmar Lapp < [hidden email]> wrote:
> >> special about this one? The file name lets me guess the input is a
> >> contig or even a full chromosome? Is the input on which the process
> >> wasn't killed of the same nature? Are the sequences of comparable or
> >> vastly different lengths? Is there only a single contig in the
> >> offending input? Can you reproduce the problem on an empty database
> >> with input containing a single entry? If so, let me know where I can
> >> get that file from and I'll try to reproduce it locally.
> >>
> >> -hilmar
> >>
> >> On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:
> >>
> >> > Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
> >> > --dbname=USBA --dbuser=postgres --format=genbank --driver=Pg --debug
> >> > NC_003076.gbk)
> >> > is getting killed after the follwoing step?
> >> >
> >> >Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer
> >> > for Bio::DB::BioSQL::BiosequenceAdaptor
> >> > preparing SELECT statement: SELECT bioentry_id FROM biosequence
> >> WHERE
> >> > bioentry_id = ?
> >> >
> >> > Killed
> >> >
> >> > I'm using a linux box. This didn't happen for a different i/p file!
> >> >
> >> > Thanks,
> >> > Angshu
> >> >
> >> >
> >> > On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm sorry that
> >> I
> >> > missed it! Thanks for pointing it out.
> >> >> Also thanks Hilmar for the update.
> >> >>
> >> >> Angshu
> >> >>
> >> >>
> >> >> On 12/29/05, Torsten Seemann <
> >> [hidden email]
> >> >> > wrote:> I'm getting the following error while trying to run :
> >> >>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
> >> >>> postgres -format
> >> >>> > genbank NC_003076.gbk
> >> >>> > MSG: failed to open connection: Can't connect to local MySQL
> >> >>> server through
> >> >>> > socket '/var/lib/mysql/mysql.sock' (2)
> >> >>> > But I've a postgreSQL db and not a MySQL one...could anyone
> >> please
> >> >>> guide me
> >> >>> > troubleshoot this?
> >> >>>
> >> >>> Did you read the documentation for the load_seqdatabase.pl script?
> >> >>>
> >> >>> It's in the script itself!
> >> >>>
> >> >>> =item --driver $driver
> >> >>> the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
> >> >>> [mysql]
> >> >>>
> >> >>> The default DBI driver is [mysql].
> >> >>>
> >> >>> I think you want the option "-driver Pg".
> >> >>>
> >>  >>> --
> >> >>> Torsten Seemann
> >> >>> Victorian Bioinformatics Consortium, Monash University, Australia
> >> >>> http://www.vicbioinformatics.com/
> >> >>
> >> >>
> >> --
> >> -------------------------------------------------------------
> >> Hilmar Lappemail: lapp at gnf.org
> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> -------------------------------------------------------------
> >>
> >>
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>

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Re: error running load_seqdatabase.pl

Hilmar Lapp
Why don't you just ask your sysadmin - he'll know where to look. It's
actually in a config file, and the default installation of Postgres
makes this config file unreadable for every one except the pg-admin
user chosen at installation time.

        -hilmar

On Dec 30, 2005, at 3:15 PM, Angshu Kar wrote:

> I've no clue about my Pg setup! It has been done by the sysadmin! :(
> Could you please tell me the commands and I can run and let you know
> the reports?
>
> thanks,
> angshu
>
> On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
>>
>> Also, you haven't reported your hw setup. In particular, how much
>> memory and swap do you have, is Pg running locally (your command line
>> suggests it does), and how much memory have you allocated to Pg?
>>
>>         -hilmar
>>
>> On Dec 30, 2005, at 3:01 PM, Angshu Kar wrote:
>>
>> > Yes Hilmar its indeed a full sequence of chromosome. I got it from
>> > ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
>> > I tried with the .faa and .fna files and they ran successfully.
>> > Also I missed a line (may be relevant) in the debug o/p:
>> > no adaptor found for class Bio::Annotation::TypeManager
>> >
>> > Thanks,
>> > Angshu
>> >
>> >
>> > On 12/30/05, Hilmar Lapp < [hidden email]> wrote:
>> >> special about this one? The file name lets me guess the input is a
>> >> contig or even a full chromosome? Is the input on which the process
>> >> wasn't killed of the same nature? Are the sequences of comparable
>> or
>> >> vastly different lengths? Is there only a single contig in the
>> >> offending input? Can you reproduce the problem on an empty database
>> >> with input containing a single entry? If so, let me know where I
>> can
>> >> get that file from and I'll try to reproduce it locally.
>> >>
>> >> -hilmar
>> >>
>> >> On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:
>> >>
>> >> > Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
>> >> > --dbname=USBA --dbuser=postgres --format=genbank --driver=Pg
>> --debug
>> >> > NC_003076.gbk)
>> >> > is getting killed after the follwoing step?
>> >> >
>> >> >Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer
>> >> > for Bio::DB::BioSQL::BiosequenceAdaptor
>> >> > preparing SELECT statement: SELECT bioentry_id FROM biosequence
>> >> WHERE
>> >> > bioentry_id = ?
>> >> >
>> >> > Killed
>> >> >
>> >> > I'm using a linux box. This didn't happen for a different i/p
>> file!
>> >> >
>> >> > Thanks,
>> >> > Angshu
>> >> >
>> >> >
>> >> > On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm sorry
>> that
>> >> I
>> >> > missed it! Thanks for pointing it out.
>> >> >> Also thanks Hilmar for the update.
>> >> >>
>> >> >> Angshu
>> >> >>
>> >> >>
>>  >> >> On 12/29/05, Torsten Seemann <
>> >> [hidden email]
>> >> >> > wrote:> I'm getting the following error while trying to run :
>> >> >>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
>> >> >>> postgres -format
>> >> >>> > genbank NC_003076.gbk
>> >> >>> > MSG: failed to open connection: Can't connect to local MySQL
>> >> >>> server through
>> >> >>> > socket '/var/lib/mysql/mysql.sock' (2)
>> >> >>> > But I've a postgreSQL db and not a MySQL one...could anyone
>> >> please
>>  >> >>> guide me
>> >> >>> > troubleshoot this?
>> >> >>>
>> >> >>> Did you read the documentation for the load_seqdatabase.pl
>> script?
>> >> >>>
>> >> >>> It's in the script itself!
>> >> >>>
>> >> >>> =item --driver $driver
>> >> >>> the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
>> >> >>> [mysql]
>> >> >>>
>> >> >>> The default DBI driver is [mysql].
>> >> >>>
>> >> >>> I think you want the option "-driver Pg".
>> >> >>>
>> >>  >>> --
>> >> >>> Torsten Seemann
>> >> >>> Victorian Bioinformatics Consortium, Monash University,
>> Australia
>> >> >>> http://www.vicbioinformatics.com/
>> >> >>
>> >> >>
>> >> --
>> >> -------------------------------------------------------------
>> >> Hilmar Lappemail: lapp at gnf.org
>> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> -------------------------------------------------------------
>> >>
>> >>
>> >
>> >
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



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Re: error running load_seqdatabase.pl

Angshu Kar
oops! he is not present now!
anyways, if you have some time could you please if there are any reasons for
the script to get killed with the .gbk file?

Thanks,
Angshu

On 12/30/05, Hilmar Lapp <[hidden email]> wrote:

>
> Why don't you just ask your sysadmin - he'll know where to look. It's
> actually in a config file, and the default installation of Postgres
> makes this config file unreadable for every one except the pg-admin
> user chosen at installation time.
>
>         -hilmar
>
> On Dec 30, 2005, at 3:15 PM, Angshu Kar wrote:
>
> > I've no clue about my Pg setup! It has been done by the sysadmin! :(
> > Could you please tell me the commands and I can run and let you know
> > the reports?
> >
> > thanks,
> > angshu
> >
> > On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
> >>
> >> Also, you haven't reported your hw setup. In particular, how much
> >> memory and swap do you have, is Pg running locally (your command line
> >> suggests it does), and how much memory have you allocated to Pg?
> >>
> >> -hilmar
> >>
> >> On Dec 30, 2005, at 3:01 PM, Angshu Kar wrote:
> >>
> >> > Yes Hilmar its indeed a full sequence of chromosome. I got it from
> >> > ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
> >> > I tried with the .faa and .fna files and they ran successfully.
> >> > Also I missed a line (may be relevant) in the debug o/p:
> >> > no adaptor found for class Bio::Annotation::TypeManager
> >> >
> >> > Thanks,
> >> > Angshu
> >> >
> >> >
> >> > On 12/30/05, Hilmar Lapp < [hidden email]> wrote:
> >> >> special about this one? The file name lets me guess the input is a
> >> >> contig or even a full chromosome? Is the input on which the process
> >> >> wasn't killed of the same nature? Are the sequences of comparable
> >> or
> >> >> vastly different lengths? Is there only a single contig in the
> >> >> offending input? Can you reproduce the problem on an empty database
> >> >> with input containing a single entry? If so, let me know where I
> >> can
> >> >> get that file from and I'll try to reproduce it locally.
> >> >>
> >> >> -hilmar
> >> >>
> >> >> On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:
> >> >>
> >> >> > Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
> >> >> > --dbname=USBA --dbuser=postgres --format=genbank --driver=Pg
> >> --debug
> >> >> > NC_003076.gbk)
> >> >> > is getting killed after the follwoing step?
> >> >> >
> >> >> >Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer
> >> >> > for Bio::DB::BioSQL::BiosequenceAdaptor
> >> >> > preparing SELECT statement: SELECT bioentry_id FROM biosequence
> >> >> WHERE
> >> >> > bioentry_id = ?
> >> >> >
> >> >> > Killed
> >> >> >
> >> >> > I'm using a linux box. This didn't happen for a different i/p
> >> file!
> >> >> >
> >> >> > Thanks,
> >> >> > Angshu
> >> >> >
> >> >> >
> >> >> > On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm sorry
> >> that
> >> >> I
> >> >> > missed it! Thanks for pointing it out.
> >> >> >> Also thanks Hilmar for the update.
> >> >> >>
> >> >> >> Angshu
> >> >> >>
> >> >> >>
> >>  >> >> On 12/29/05, Torsten Seemann <
> >> >> [hidden email]
> >> >> >> > wrote:> I'm getting the following error while trying to run :
> >> >> >>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
> >> >> >>> postgres -format
> >> >> >>> > genbank NC_003076.gbk
> >> >> >>> > MSG: failed to open connection: Can't connect to local MySQL
> >> >> >>> server through
> >> >> >>> > socket '/var/lib/mysql/mysql.sock' (2)
> >> >> >>> > But I've a postgreSQL db and not a MySQL one...could anyone
> >> >> please
> >>  >> >>> guide me
> >> >> >>> > troubleshoot this?
> >> >> >>>
> >> >> >>> Did you read the documentation for the load_seqdatabase.pl
> >> script?
> >> >> >>>
> >> >> >>> It's in the script itself!
> >> >> >>>
> >> >> >>> =item --driver $driver
> >> >> >>> the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
> >> >> >>> [mysql]
> >> >> >>>
> >> >> >>> The default DBI driver is [mysql].
> >> >> >>>
> >> >> >>> I think you want the option "-driver Pg".
> >> >> >>>
> >> >>>>> --
> >> >> >>> Torsten Seemann
> >> >> >>> Victorian Bioinformatics Consortium, Monash University,
> >> Australia
> >> >> >>> http://www.vicbioinformatics.com/
> >> >> >>
> >> >> >>
> >> >> --
> >> >> -------------------------------------------------------------
> >> >> Hilmar Lappemail: lapp at gnf.org
> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> >> -------------------------------------------------------------
> >> >>
> >> >>
> >> >
> >> >
> >> --
> >> -------------------------------------------------------------
> >> Hilmar Lappemail: lapp at gnf.org
> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> -------------------------------------------------------------
> >>
> >>
> >>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>

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Re: error running load_seqdatabase.pl

Hilmar Lapp
I suspect it's either a (out-of-)memory error or a binary
incompatibility.

You haven't yet run the bioperl-db test suite, have you? Please don't
ask for more help before you haven't done that.

Also, you do remember my earlier answer to a similar report from you,
right?
http://portal.open-bio.org/pipermail/bioperl-l/2005-December/020389.html

The two first things to do is to check whether you run out of shared
memory and to run the tests and see whether the location where the
process gets killed can be narrowed down. If it's not a bug (which it
is unlikely to be - but the tests will provide more evidence) then the
next step would be to recompile your own perl, DBI and DBD::Pg, and
PostgreSQL, in that order.

        -hilmar

On Dec 30, 2005, at 4:13 PM, Angshu Kar wrote:

> oops! he is not present now!
> anyways, if you have some time could you please if there are any
> reasons for the script to get killed with the .gbk file?
>
> Thanks,
> Angshu
>
> On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
>> actually in a config file, and the default installation of Postgres
>> makes this config file unreadable for every one except the pg-admin
>> user chosen at installation time.
>>
>>         -hilmar
>>
>> On Dec 30, 2005, at 3:15 PM, Angshu Kar wrote:
>>
>> > I've no clue about my Pg setup! It has been done by the sysadmin! :(
>> > Could you please tell me the commands and I can run and let you know
>> > the reports?
>> >
>> > thanks,
>> > angshu
>> >
>> > On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
>> >>
>> >> Also, you haven't reported your hw setup. In particular, how much
>> >> memory and swap do you have, is Pg running locally (your command
>> line
>> >> suggests it does), and how much memory have you allocated to Pg?
>> >>
>> >> -hilmar
>> >>
>> >> On Dec 30, 2005, at 3:01 PM, Angshu Kar wrote:
>> >>
>> >> > Yes Hilmar its indeed a full sequence of chromosome. I got it
>> from
>> >> > ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
>> >> > I tried with the .faa and .fna files and they ran successfully.
>> >> > Also I missed a line (may be relevant) in the debug o/p:
>> >> > no adaptor found for class Bio::Annotation::TypeManager
>> >> >
>> >> > Thanks,
>> >> > Angshu
>> >> >
>> >> >
>> >> > On 12/30/05, Hilmar Lapp < [hidden email]> wrote:
>> >> >> special about this one? The file name lets me guess the input
>> is a
>> >> >> contig or even a full chromosome? Is the input on which the
>> process
>> >> >> wasn't killed of the same nature? Are the sequences of
>> comparable
>> >> or
>> >> >> vastly different lengths? Is there only a single contig in the
>> >> >> offending input? Can you reproduce the problem on an empty
>> database
>> >> >> with input containing a single entry? If so, let me know where I
>> >> can
>> >> >> get that file from and I'll try to reproduce it locally.
>> >> >>
>> >> >> -hilmar
>> >> >>
>> >> >> On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:
>> >> >>
>> >> >> > Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
>> >> >> > --dbname=USBA --dbuser=postgres --format=genbank --driver=Pg
>> >> --debug
>> >> >> > NC_003076.gbk)
>> >> >> > is getting killed after the follwoing step?
>>  >> >> >
>> >> >> >Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver
>> peer
>> >> >> > for Bio::DB::BioSQL::BiosequenceAdaptor
>> >> >> > preparing SELECT statement: SELECT bioentry_id FROM
>> biosequence
>> >> >> WHERE
>> >> >> > bioentry_id = ?
>> >> >> >
>> >> >> > Killed
>> >> >> >
>> >> >> > I'm using a linux box. This didn't happen for a different i/p
>> >> file!
>> >> >> >
>> >> >> > Thanks,
>> >> >> > Angshu
>> >> >> >
>> >> >> >
>> >> >> > On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm sorry
>> >> that
>> >> >> I
>> >> >> > missed it! Thanks for pointing it out.
>> >> >> >> Also thanks Hilmar for the update.
>> >> >> >>
>> >> >> >> Angshu
>> >> >> >>
>> >> >> >>
>> >>  >> >> On 12/29/05, Torsten Seemann <
>> >> >> [hidden email]
>> >> >> >> > wrote:> I'm getting the following error while trying to
>> run :
>> >> >> >>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
>> >> >> >>> postgres -format
>> >> >> >>> > genbank NC_003076.gbk
>> >> >> >>> > MSG: failed to open connection: Can't connect to local
>> MySQL
>> >> >> >>> server through
>> >> >> >>> > socket '/var/lib/mysql/mysql.sock' (2)
>> >> >> >>> > But I've a postgreSQL db and not a MySQL one...could
>> anyone
>> >> >> please
>> >>  >> >>> guide me
>> >> >> >>> > troubleshoot this?
>> >> >> >>>
>> >> >> >>> Did you read the documentation for the load_seqdatabase.pl
>> >> script?
>> >> >> >>>
>> >> >> >>> It's in the script itself!
>> >> >> >>>
>> >> >> >>> =item --driver $driver
>> >> >> >>> the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
>> >> >> >>> [mysql]
>> >> >> >>>
>> >> >> >>> The default DBI driver is [mysql].
>> >> >> >>>
>> >> >> >>> I think you want the option "-driver Pg".
>> >> >> >>>
>> >> >>>>> --
>> >> >> >>> Torsten Seemann
>> >> >> >>> Victorian Bioinformatics Consortium, Monash University,
>> >> Australia
>> >> >> >>> http://www.vicbioinformatics.com/
>> >> >> >>
>> >> >> >>
>> >> >> --
>> >> >> -------------------------------------------------------------
>> >> >> Hilmar Lappemail: lapp at gnf.org
>> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> >> -------------------------------------------------------------
>> >> >>
>> >> >>
>> >> >
>> >> >
>> >> --
>> >> -------------------------------------------------------------
>> >> Hilmar Lappemail: lapp at gnf.org
>> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> -------------------------------------------------------------
>> >>
>> >>
>> >>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



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Re: error running load_seqdatabase.pl

Angshu Kar
A new error:

I installed bioperl-db in my own WinXP m/c following instructions in CVS by
Chris Fields. I'm trying to run the same command from this m/c (the postgres
db resides in the linux box) and getting the error:

Loading NC_003076.gbk ...
Undefined subroutine &Bio::Root::Root::debug called at
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1537, <GEN0>
line 766536.

Any inputs on this?



On 12/30/05, Hilmar Lapp <[hidden email]> wrote:

>
> I suspect it's either a (out-of-)memory error or a binary
> incompatibility.
>
> You haven't yet run the bioperl-db test suite, have you? Please don't
> ask for more help before you haven't done that.
>
> Also, you do remember my earlier answer to a similar report from you,
> right?
> http://portal.open-bio.org/pipermail/bioperl-l/2005-December/020389.html
>
> The two first things to do is to check whether you run out of shared
> memory and to run the tests and see whether the location where the
> process gets killed can be narrowed down. If it's not a bug (which it
> is unlikely to be - but the tests will provide more evidence) then the
> next step would be to recompile your own perl, DBI and DBD::Pg, and
> PostgreSQL, in that order.
>
>         -hilmar
>
> On Dec 30, 2005, at 4:13 PM, Angshu Kar wrote:
>
> > oops! he is not present now!
> > anyways, if you have some time could you please if there are any
> > reasons for the script to get killed with the .gbk file?
> >
> > Thanks,
> > Angshu
> >
> > On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
> >> actually in a config file, and the default installation of Postgres
> >> makes this config file unreadable for every one except the pg-admin
> >> user chosen at installation time.
> >>
> >> -hilmar
> >>
> >> On Dec 30, 2005, at 3:15 PM, Angshu Kar wrote:
> >>
> >> > I've no clue about my Pg setup! It has been done by the sysadmin! :(
> >> > Could you please tell me the commands and I can run and let you know
> >> > the reports?
> >> >
> >> > thanks,
> >> > angshu
> >> >
> >> > On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
> >> >>
> >> >> Also, you haven't reported your hw setup. In particular, how much
> >> >> memory and swap do you have, is Pg running locally (your command
> >> line
> >> >> suggests it does), and how much memory have you allocated to Pg?
> >> >>
> >> >> -hilmar
> >> >>
> >> >> On Dec 30, 2005, at 3:01 PM, Angshu Kar wrote:
> >> >>
> >> >> > Yes Hilmar its indeed a full sequence of chromosome. I got it
> >> from
> >> >> > ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
> >> >> > I tried with the .faa and .fna files and they ran successfully.
> >> >> > Also I missed a line (may be relevant) in the debug o/p:
> >> >> > no adaptor found for class Bio::Annotation::TypeManager
> >> >> >
> >> >> > Thanks,
> >> >> > Angshu
> >> >> >
> >> >> >
> >> >> > On 12/30/05, Hilmar Lapp < [hidden email]> wrote:
> >> >> >> special about this one? The file name lets me guess the input
> >> is a
> >> >> >> contig or even a full chromosome? Is the input on which the
> >> process
> >> >> >> wasn't killed of the same nature? Are the sequences of
> >> comparable
> >> >> or
> >> >> >> vastly different lengths? Is there only a single contig in the
> >> >> >> offending input? Can you reproduce the problem on an empty
> >> database
> >> >> >> with input containing a single entry? If so, let me know where I
> >> >> can
> >> >> >> get that file from and I'll try to reproduce it locally.
> >> >> >>
> >> >> >> -hilmar
> >> >> >>
> >> >> >> On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:
> >> >> >>
> >> >> >> > Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
> >> >> >> > --dbname=USBA --dbuser=postgres --format=genbank --driver=Pg
> >> >> --debug
> >> >> >> > NC_003076.gbk)
> >> >> >> > is getting killed after the follwoing step?
> >>  >> >> >
> >> >> >> >Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver
> >> peer
> >> >> >> > for Bio::DB::BioSQL::BiosequenceAdaptor
> >> >> >> > preparing SELECT statement: SELECT bioentry_id FROM
> >> biosequence
> >> >> >> WHERE
> >> >> >> > bioentry_id = ?
> >> >> >> >
> >> >> >> > Killed
> >> >> >> >
> >> >> >> > I'm using a linux box. This didn't happen for a different i/p
> >> >> file!
> >> >> >> >
> >> >> >> > Thanks,
> >> >> >> > Angshu
> >> >> >> >
> >> >> >> >
> >> >> >> > On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm sorry
> >> >> that
> >> >> >> I
> >> >> >> > missed it! Thanks for pointing it out.
> >> >> >> >> Also thanks Hilmar for the update.
> >> >> >> >>
> >> >> >> >> Angshu
> >> >> >> >>
> >> >> >> >>
> >> >>>> >> On 12/29/05, Torsten Seemann <
> >> >> >> [hidden email]
> >> >> >> >> > wrote:> I'm getting the following error while trying to
> >> run :
> >> >> >> >>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
> >> >> >> >>> postgres -format
> >> >> >> >>> > genbank NC_003076.gbk
> >> >> >> >>> > MSG: failed to open connection: Can't connect to local
> >> MySQL
> >> >> >> >>> server through
> >> >> >> >>> > socket '/var/lib/mysql/mysql.sock' (2)
> >> >> >> >>> > But I've a postgreSQL db and not a MySQL one...could
> >> anyone
> >> >> >> please
> >> >>>> >>> guide me
> >> >> >> >>> > troubleshoot this?
> >> >> >> >>>
> >> >> >> >>> Did you read the documentation for the load_seqdatabase.pl
> >> >> script?
> >> >> >> >>>
> >> >> >> >>> It's in the script itself!
> >> >> >> >>>
> >> >> >> >>> =item --driver $driver
> >> >> >> >>> the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
> >> >> >> >>> [mysql]
> >> >> >> >>>
> >> >> >> >>> The default DBI driver is [mysql].
> >> >> >> >>>
> >> >> >> >>> I think you want the option "-driver Pg".
> >> >> >> >>>
> >> >> >>>>> --
> >> >> >> >>> Torsten Seemann
> >> >> >> >>> Victorian Bioinformatics Consortium, Monash University,
> >> >> Australia
> >> >> >> >>> http://www.vicbioinformatics.com/
> >> >> >> >>
> >> >> >> >>
> >> >> >> --
> >> >> >> -------------------------------------------------------------
> >> >> >> Hilmar Lappemail: lapp at gnf.org
> >> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> >> >> -------------------------------------------------------------
> >> >> >>
> >> >> >>
> >> >> >
> >> >> >
> >> >> --
> >> >> -------------------------------------------------------------
> >> >> Hilmar Lappemail: lapp at gnf.org
> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> >> -------------------------------------------------------------
> >> >>
> >> >>
> >> >>
> >> --
> >> -------------------------------------------------------------
> >> Hilmar Lappemail: lapp at gnf.org
> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> -------------------------------------------------------------
> >>
> >>
> >>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>

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Re: error running load_seqdatabase.pl

Angshu Kar
In reply to this post by Hilmar Lapp
Hi Hilmar,

All my tests failed for my WInXP m/c!I'm really at a fix!:(
Do I need to uninstall bioperl-db, bioperl and even perl??? How to do that?
Please guide.
I'll be obliged if anyone with WinXp (not cygwin) provides his/her feedback
...

Thanks,
Angshu

Microsoft (R) Program Maintenance Utility   Version 1.50
Copyright (c) Microsoft Corp 1988-94. All rights reserved.

        C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0,
'bl
ib\lib', 'blib\arch')" t\01dbadaptor.t t\02species.t t\03simpleseq.t
t\04swiss.t
 t\05seqfeature.t t\06comment.t t\07dblink.t t\08genbank.t t\09fuzzy2.t
t\10ense
mbl.t t\11locuslink.t t\12ontology.t t\13remove.t t\14query.t t\15cluster.t
t\01dbadaptor.....driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at
t\01dbadaptor.t
line 20
t\01dbadaptor.....dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-19
        Failed 19/19 tests, 0.00% okay
t\02species.......driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at
t\02species.t li
ne 18
t\02species.......dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-65
        Failed 65/65 tests, 0.00% okay
t\03simpleseq.....driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at
t\03simpleseq.t
line 19
t\03simpleseq.....dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-59
        Failed 59/59 tests, 0.00% okay
t\04swiss.........driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at t\04swiss.t
line
 20
t\04swiss.........dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-52
        Failed 52/52 tests, 0.00% okay
t\05seqfeature....driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at
t\05seqfeature.t
 line 19
t\05seqfeature....dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-48
        Failed 48/48 tests, 0.00% okay
t\06comment.......driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at
t\06comment.t li
ne 20
t\06comment.......dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-11
        Failed 11/11 tests, 0.00% okay
t\07dblink........driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at t\07dblink.t
lin
e 21
t\07dblink........dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-18
        Failed 18/18 tests, 0.00% okay
t\08genbank.......driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at
t\08genbank.t li
ne 21
t\08genbank.......dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-18
        Failed 18/18 tests, 0.00% okay
t\09fuzzy2........driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at t\09fuzzy2.t
lin
e 26
t\09fuzzy2........dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-21
        Failed 21/21 tests, 0.00% okay
t\10ensembl.......driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at
t\10ensembl.t li
ne 21
t\10ensembl.......dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-15
        Failed 15/15 tests, 0.00% okay
t\11locuslink.....driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at
t\11locuslink.t
line 21
t\11locuslink.....dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-110
        Failed 110/110 tests, 0.00% okay
t\12ontology......driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at
t\12ontology.t l
ine 19
t\12ontology......dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-738
        Failed 738/738 tests, 0.00% okay
t\13remove........driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at t\13remove.t
lin
e 19
t\13remove........dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-59
        Failed 59/59 tests, 0.00% okay
t\14query.........ok
t\15cluster.......driver not set at t/DBTestHarness.pm line 106
        DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called at
t/DBTest
Harness.pm line 204
        DBTestHarness::create_db('DBTestHarness=HASH(0x235278)') called at
t/DBT
estHarness.pm line 94
        DBTestHarness::new('DBTestHarness', 'biosql') called at
t\15cluster.t li
ne 19
t\15cluster.......dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-160
        Failed 160/160 tests, 0.00% okay
Failed Test      Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t\01dbadaptor.t     2   512    19   38 200.00%  1-19
t\02species.t       2   512    65  130 200.00%  1-65
t\03simpleseq.t     2   512    59  118 200.00%  1-59
t\04swiss.t         2   512    52  104 200.00%  1-52
t\05seqfeature.t    2   512    48   96 200.00%  1-48
t\06comment.t       2   512    11   22 200.00%  1-11
t\07dblink.t        2   512    18   36 200.00%  1-18
t\08genbank.t       2   512    18   36 200.00%  1-18
t\09fuzzy2.t        2   512    21   42 200.00%  1-21
t\10ensembl.t       2   512    15   30 200.00%  1-15
t\11locuslink.t     2   512   110  220 200.00%  1-110
t\12ontology.t      2   512   738 1476 200.00%  1-738
t\13remove.t        2   512    59  118 200.00%  1-59
t\15cluster.t       2   512   160  320 200.00%  1-160
Failed 14/15 test scripts, 6.67% okay. 1393/1411 subtests failed, 1.28%okay.
NMAKE : fatal error U1077: 'C:\WINDOWS\system32\cmd.exe' : return code '0x2'
Stop.

On 12/30/05, Hilmar Lapp <[hidden email]> wrote:

>
> I suspect it's either a (out-of-)memory error or a binary
> incompatibility.
>
> You haven't yet run the bioperl-db test suite, have you? Please don't
> ask for more help before you haven't done that.
>
> Also, you do remember my earlier answer to a similar report from you,
> right?
> http://portal.open-bio.org/pipermail/bioperl-l/2005-December/020389.html
>
> The two first things to do is to check whether you run out of shared
> memory and to run the tests and see whether the location where the
> process gets killed can be narrowed down. If it's not a bug (which it
> is unlikely to be - but the tests will provide more evidence) then the
> next step would be to recompile your own perl, DBI and DBD::Pg, and
> PostgreSQL, in that order.
>
>         -hilmar
>
> On Dec 30, 2005, at 4:13 PM, Angshu Kar wrote:
>
> > oops! he is not present now!
> > anyways, if you have some time could you please if there are any
> > reasons for the script to get killed with the .gbk file?
> >
> > Thanks,
> > Angshu
> >
> > On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
> >> actually in a config file, and the default installation of Postgres
> >> makes this config file unreadable for every one except the pg-admin
> >> user chosen at installation time.
> >>
> >> -hilmar
> >>
> >> On Dec 30, 2005, at 3:15 PM, Angshu Kar wrote:
> >>
> >> > I've no clue about my Pg setup! It has been done by the sysadmin! :(
> >> > Could you please tell me the commands and I can run and let you know
> >> > the reports?
> >> >
> >> > thanks,
> >> > angshu
> >> >
> >> > On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
> >> >>
> >> >> Also, you haven't reported your hw setup. In particular, how much
> >> >> memory and swap do you have, is Pg running locally (your command
> >> line
> >> >> suggests it does), and how much memory have you allocated to Pg?
> >> >>
> >> >> -hilmar
> >> >>
> >> >> On Dec 30, 2005, at 3:01 PM, Angshu Kar wrote:
> >> >>
> >> >> > Yes Hilmar its indeed a full sequence of chromosome. I got it
> >> from
> >> >> > ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
> >> >> > I tried with the .faa and .fna files and they ran successfully.
> >> >> > Also I missed a line (may be relevant) in the debug o/p:
> >> >> > no adaptor found for class Bio::Annotation::TypeManager
> >> >> >
> >> >> > Thanks,
> >> >> > Angshu
> >> >> >
> >> >> >
> >> >> > On 12/30/05, Hilmar Lapp < [hidden email]> wrote:
> >> >> >> special about this one? The file name lets me guess the input
> >> is a
> >> >> >> contig or even a full chromosome? Is the input on which the
> >> process
> >> >> >> wasn't killed of the same nature? Are the sequences of
> >> comparable
> >> >> or
> >> >> >> vastly different lengths? Is there only a single contig in the
> >> >> >> offending input? Can you reproduce the problem on an empty
> >> database
> >> >> >> with input containing a single entry? If so, let me know where I
> >> >> can
> >> >> >> get that file from and I'll try to reproduce it locally.
> >> >> >>
> >> >> >> -hilmar
> >> >> >>
> >> >> >> On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:
> >> >> >>
> >> >> >> > Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
> >> >> >> > --dbname=USBA --dbuser=postgres --format=genbank --driver=Pg
> >> >> --debug
> >> >> >> > NC_003076.gbk)
> >> >> >> > is getting killed after the follwoing step?
> >>  >> >> >
> >> >> >> >Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver
> >> peer
> >> >> >> > for Bio::DB::BioSQL::BiosequenceAdaptor
> >> >> >> > preparing SELECT statement: SELECT bioentry_id FROM
> >> biosequence
> >> >> >> WHERE
> >> >> >> > bioentry_id = ?
> >> >> >> >
> >> >> >> > Killed
> >> >> >> >
> >> >> >> > I'm using a linux box. This didn't happen for a different i/p
> >> >> file!
> >> >> >> >
> >> >> >> > Thanks,
> >> >> >> > Angshu
> >> >> >> >
> >> >> >> >
> >> >> >> > On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm sorry
> >> >> that
> >> >> >> I
> >> >> >> > missed it! Thanks for pointing it out.
> >> >> >> >> Also thanks Hilmar for the update.
> >> >> >> >>
> >> >> >> >> Angshu
> >> >> >> >>
> >> >> >> >>
> >> >>>> >> On 12/29/05, Torsten Seemann <
> >> >> >> [hidden email]
> >> >> >> >> > wrote:> I'm getting the following error while trying to
> >> run :
> >> >> >> >>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser
> >> >> >> >>> postgres -format
> >> >> >> >>> > genbank NC_003076.gbk
> >> >> >> >>> > MSG: failed to open connection: Can't connect to local
> >> MySQL
> >> >> >> >>> server through
> >> >> >> >>> > socket '/var/lib/mysql/mysql.sock' (2)
> >> >> >> >>> > But I've a postgreSQL db and not a MySQL one...could
> >> anyone
> >> >> >> please
> >> >>>> >>> guide me
> >> >> >> >>> > troubleshoot this?
> >> >> >> >>>
> >> >> >> >>> Did you read the documentation for the load_seqdatabase.pl
> >> >> script?
> >> >> >> >>>
> >> >> >> >>> It's in the script itself!
> >> >> >> >>>
> >> >> >> >>> =item --driver $driver
> >> >> >> >>> the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle
> >> >> >> >>> [mysql]
> >> >> >> >>>
> >> >> >> >>> The default DBI driver is [mysql].
> >> >> >> >>>
> >> >> >> >>> I think you want the option "-driver Pg".
> >> >> >> >>>
> >> >> >>>>> --
> >> >> >> >>> Torsten Seemann
> >> >> >> >>> Victorian Bioinformatics Consortium, Monash University,
> >> >> Australia
> >> >> >> >>> http://www.vicbioinformatics.com/
> >> >> >> >>
> >> >> >> >>
> >> >> >> --
> >> >> >> -------------------------------------------------------------
> >> >> >> Hilmar Lappemail: lapp at gnf.org
> >> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> >> >> -------------------------------------------------------------
> >> >> >>
> >> >> >>
> >> >> >
> >> >> >
> >> >> --
> >> >> -------------------------------------------------------------
> >> >> Hilmar Lappemail: lapp at gnf.org
> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> >> -------------------------------------------------------------
> >> >>
> >> >>
> >> >>
> >> --
> >> -------------------------------------------------------------
> >> Hilmar Lappemail: lapp at gnf.org
> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
> >> -------------------------------------------------------------
> >>
> >>
> >>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>

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http://portal.open-bio.org/mailman/listinfo/bioperl-l
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Open this post in threaded view
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Re: error running load_seqdatabase.pl

Hilmar Lapp
Angshu, next time you feel the urge to write such an email restrain  
yourself, hold off, sit back, and, most importantly, think.

The error message clearly says 'driver not set'. Did you do anything  
that assures you that you *have* set the driver?

I suppose you forgot to follow the instructions for running the tests,  
namely to copy
t/DBHarness.conf.example to t/DBHarness.biosql.conf, and edit to suit  
your setup. This is documented, and I told you about this step earlier.

        -hilmar

On Dec 30, 2005, at 5:59 PM, Angshu Kar wrote:

> Hi Hilmar,
>
> All my tests failed for my WInXP m/c!I'm really at a fix!:(
> Do I need to uninstall bioperl-db, bioperl and even perl??? How to do  
> that?
> Please guide.
> I'll be obliged if anyone with WinXp (not cygwin) provides his/her  
> feedback ...
>
> Thanks,
> Angshu
>
> Microsoft (R) Program Maintenance Utility   Version 1.50
> Copyright (c) Microsoft Corp 1988-94. All rights reserved.
>
>         C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e"  
> "test_harness(0, 'bl
> ib\lib', 'blib\arch')" t\01dbadaptor.t t\02species.t t\03simpleseq.t  
> t\04swiss.t
>  t\05seqfeature.t t\06comment.t t\07dblink.t t\08genbank.t  
> t\09fuzzy2.t t\10ense
> mbl.t t\11locuslink.t t\12ontology.t t\13remove.t t\14query.t  
> t\15cluster.t
>  t\01dbadaptor.....driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\01dbadaptor.t
> line 20
> t\01dbadaptor.....dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-19
>         Failed 19/19 tests, 0.00% okay
> t\02species.......driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\02species.t li
> ne 18
> t\02species.......dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-65
>         Failed 65/65 tests, 0.00% okay
> t\03simpleseq.....driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\03simpleseq.t
> line 19
> t\03simpleseq.....dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-59
>         Failed 59/59 tests, 0.00% okay
> t\04swiss.........driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\04swiss.t line
>  20
> t\04swiss.........dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-52
>         Failed 52/52 tests, 0.00% okay
> t\05seqfeature....driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\05seqfeature.t
>  line 19
> t\05seqfeature....dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-48
>         Failed 48/48 tests, 0.00% okay
> t\06comment.......driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\06comment.t li
> ne 20
> t\06comment.......dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-11
>         Failed 11/11 tests, 0.00% okay
> t\07dblink........driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\07dblink.t lin
> e 21
> t\07dblink........dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-18
>         Failed 18/18 tests, 0.00% okay
> t\08genbank.......driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\08genbank.t li
> ne 21
> t\08genbank.......dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-18
>         Failed 18/18 tests, 0.00% okay
> t\09fuzzy2........driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\09fuzzy2.t lin
> e 26
> t\09fuzzy2........dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-21
>         Failed 21/21 tests, 0.00% okay
> t\10ensembl.......driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\10ensembl.t li
> ne 21
> t\10ensembl.......dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-15
>         Failed 15/15 tests, 0.00% okay
> t\11locuslink.....driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\11locuslink.t
> line 21
> t\11locuslink.....dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-110
>         Failed 110/110 tests, 0.00% okay
> t\12ontology......driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\12ontology.t l
> ine 19
> t\12ontology......dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-738
>         Failed 738/738 tests, 0.00% okay
> t\13remove........driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\13remove.t lin
> e 19
> t\13remove........dubious
>          Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-59
>         Failed 59/59 tests, 0.00% okay
> t\14query.........ok
> t\15cluster.......driver not set at t/DBTestHarness.pm line 106
>         DBTestHarness::driver('DBTestHarness=HASH(0x235278)') called  
> at t/DBTest
> Harness.pm line 204
>         DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')  
> called at t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness', 'biosql') called at  
> t\15cluster.t li
> ne 19
> t\15cluster.......dubious
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-160
>         Failed 160/160 tests, 0.00% okay
> Failed Test      Stat Wstat Total Fail  Failed  List of Failed
> -----------------------------------------------------------------------
> --------
> t\01dbadaptor.t     2   512    19   38 200.00%  1-19
> t\02species.t       2   512    65  130 200.00%  1-65
> t\03simpleseq.t     2   512    59  118 200.00%  1-59
> t\04swiss.t         2   512    52  104 200.00%  1-52
> t\05seqfeature.t    2   512    48   96 200.00%  1-48
> t\06comment.t       2   512    11   22 200.00%  1-11
> t\07dblink.t        2   512    18   36 200.00%  1-18
> t\08genbank.t       2   512    18   36 200.00%  1-18
> t\09fuzzy2.t        2   512    21   42 200.00%  1-21
> t\10ensembl.t       2   512    15   30 200.00%  1-15
> t\11locuslink.t     2   512   110  220 200.00%  1-110
> t\12ontology.t      2   512   738 1476 200.00%  1-738
> t\13remove.t        2   512    59  118 200.00%  1-59
> t\15cluster.t       2   512   160  320 200.00%  1-160
> Failed 14/15 test scripts, 6.67% okay. 1393/1411 subtests failed,  
> 1.28% okay.
>  NMAKE : fatal error U1077: 'C:\WINDOWS\system32\cmd.exe' : return  
> code '0x2'
> Stop.
>
> On 12/30/05, Hilmar Lapp <[hidden email]> wrote:I suspect it's either a  
> (out-of-)memory error or a binary
>> incompatibility.
>>
>> You haven't yet run the bioperl-db test suite, have you? Please don't
>> ask for more help before you haven't done that.
>>
>> Also, you do remember my earlier answer to a similar report from you,
>> right?
>> http://portal.open-bio.org/pipermail/bioperl-l/2005-December/ 
>> 020389.html
>>
>> The two first things to do is to check whether you run out of shared
>> memory and to run the tests and see whether the location where the
>> process gets killed can be narrowed down. If it's not a bug (which it
>> is unlikely to be - but the tests will provide more evidence) then the
>>  next step would be to recompile your own perl, DBI and DBD::Pg, and
>> PostgreSQL, in that order.
>>
>>         -hilmar
>>
>> On Dec 30, 2005, at 4:13 PM, Angshu Kar wrote:
>>
>> > oops! he is not present now!
>> > anyways, if you have some time could you please if there are any
>> > reasons for the script to get killed with the .gbk file?
>> >
>> > Thanks,
>> > Angshu
>> >
>> > On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
>> >> actually in a config file, and the default installation of Postgres
>> >> makes this config file unreadable for every one except the pg-admin
>> >> user chosen at installation time.
>> >>
>> >> -hilmar
>> >>
>> >> On Dec 30, 2005, at 3:15 PM, Angshu Kar wrote:
>> >>
>> >> > I've no clue about my Pg setup! It has been done by the  
>> sysadmin! :(
>> >> > Could you please tell me the commands and I can run and let you  
>> know
>> >> > the reports?
>> >> >
>> >> > thanks,
>> >> > angshu
>> >> >
>> >> > On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
>> >> >>
>> >> >> Also, you haven't reported your hw setup. In particular, how  
>> much
>> >> >> memory and swap do you have, is Pg running locally (your command
>> >> line
>> >> >> suggests it does), and how much memory have you allocated to Pg?
>> >> >>
>> >> >> -hilmar
>> >> >>
>> >> >> On Dec 30, 2005, at 3:01 PM, Angshu Kar wrote:
>> >> >>
>> >> >> > Yes Hilmar its indeed a full sequence of chromosome. I got it
>> >> from
>> >> >> > ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
>> >> >> > I tried with the .faa and .fna files and they ran  
>> successfully.
>> >> >> > Also I missed a line (may be relevant) in the debug o/p:
>> >> >> > no adaptor found for class Bio::Annotation::TypeManager
>> >> >> >
>> >> >> > Thanks,
>> >> >> > Angshu
>> >> >> >
>> >> >> >
>> >> >> > On 12/30/05, Hilmar Lapp < [hidden email]> wrote:
>> >> >> >> special about this one? The file name lets me guess the input
>> >> is a
>> >> >> >> contig or even a full chromosome? Is the input on which the
>> >> process
>> >> >> >> wasn't killed of the same nature? Are the sequences of
>> >> comparable
>> >> >> or
>> >> >> >> vastly different lengths? Is there only a single contig in  
>> the
>> >> >> >> offending input? Can you reproduce the problem on an empty
>> >> database
>> >> >> >> with input containing a single entry? If so, let me know  
>> where I
>> >> >> can
>> >> >> >> get that file from and I'll try to reproduce it locally.
>> >> >> >>
>> >> >> >> -hilmar
>> >> >> >>
>> >> >> >> On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:
>> >> >> >>
>> >> >> >> > Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
>> >> >> >> > --dbname=USBA --dbuser=postgres --format=genbank  
>> --driver=Pg
>> >> >> --debug
>> >> >> >> > NC_003076.gbk)
>> >> >> >> > is getting killed after the follwoing step?
>> >>  >> >> >
>> >> >> >> >Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as  
>> driver
>> >> peer
>> >> >> >> > for Bio::DB::BioSQL::BiosequenceAdaptor
>> >> >> >> > preparing SELECT statement: SELECT bioentry_id FROM
>> >> biosequence
>> >> >> >> WHERE
>> >> >> >> > bioentry_id = ?
>> >> >> >> >
>> >> >> >> > Killed
>> >> >> >> >
>> >> >> >> > I'm using a linux box. This didn't happen for a different  
>> i/p
>> >> >> file!
>> >> >> >> >
>> >> >> >> > Thanks,
>> >> >> >> > Angshu
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm  
>> sorry
>> >> >> that
>> >> >> >> I
>> >> >> >> > missed it! Thanks for pointing it out.
>> >> >> >> >> Also thanks Hilmar for the update.
>> >> >> >> >>
>> >> >> >> >> Angshu
>> >> >> >> >>
>> >> >> >> >>
>> >> >>>> >> On 12/29/05, Torsten Seemann <
>> >> >> >> [hidden email]
>> >> >> >> >> > wrote:> I'm getting the following error while trying to
>> >> run :
>> >> >> >> >>> > ./load_seqdatabase.pl -host localhost -dbname USBA  
>> -dbuser
>> >> >> >> >>> postgres -format
>> >> >> >> >>> > genbank NC_003076.gbk
>> >> >> >> >>> > MSG: failed to open connection: Can't connect to local
>> >> MySQL
>> >> >> >> >>> server through
>> >> >> >> >>> > socket '/var/lib/mysql/mysql.sock' (2)
>> >> >> >> >>> > But I've a postgreSQL db and not a MySQL one...could
>> >> anyone
>> >> >> >> please
>> >> >>>> >>> guide me
>> >> >> >> >>> > troubleshoot this?
>> >> >> >> >>>
>> >> >> >> >>> Did you read the documentation for the  
>> load_seqdatabase.pl
>> >> >> script?
>> >> >> >> >>>
>>  >> >> >> >>> It's in the script itself!
>> >> >> >> >>>
>> >> >> >> >>> =item --driver $driver
>> >> >> >> >>> the DBI driver name for the RDBMS e.g., mysql, Pg, or  
>> Oracle
>> >> >> >> >>> [mysql]
>> >> >> >> >>>
>> >> >> >> >>> The default DBI driver is [mysql].
>> >> >> >> >>>
>> >> >> >> >>> I think you want the option "-driver Pg".
>> >> >> >> >>>
>> >> >> >>>>> --
>> >> >> >> >>> Torsten Seemann
>> >> >> >> >>> Victorian Bioinformatics Consortium, Monash University,
>> >> >> Australia
>> >> >> >> >>> http://www.vicbioinformatics.com/
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> --
>> >> >> >> -------------------------------------------------------------
>> >> >> >> Hilmar Lappemail: lapp at gnf.org
>> >> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> >> >> -------------------------------------------------------------
>> >> >> >>
>> >> >> >>
>> >> >> >
>> >> >> >
>> >> >> --
>> >> >> -------------------------------------------------------------
>> >> >> Hilmar Lappemail: lapp at gnf.org
>> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> >> -------------------------------------------------------------
>> >> >>
>> >> >>
>> >> >>
>> >> --
>> >> -------------------------------------------------------------
>> >> Hilmar Lappemail: lapp at gnf.org
>> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> -------------------------------------------------------------
>> >>
>> >>
>> >>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



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Re: error running load_seqdatabase.pl

Hilmar Lapp
In reply to this post by Angshu Kar
Did you set your PERL5LIB appropriately?

On some Windows platforms there are known problems with dynamically  
loaded perl modules. The module quoted below does 'use  
Bio::Root::Root;', so the absence of that is not the problem.

        -hilmar

On Dec 30, 2005, at 5:28 PM, Angshu Kar wrote:

> A new error:
>
> I installed bioperl-db in my own WinXP m/c following instructions in  
> CVS by Chris Fields. I'm trying to run the same command from this m/c  
> (the postgres db resides in the linux box) and getting the error:
>
> Loading NC_003076.gbk ...
> Undefined subroutine &Bio::Root::Root::debug called at  
> C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1537,  
> <GEN0> line 766536.
>
> Any inputs on this?
>
>
>
> On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
>> incompatibility.
>>
>> You haven't yet run the bioperl-db test suite, have you? Please don't
>> ask for more help before you haven't done that.
>>
>> Also, you do remember my earlier answer to a similar report from you,
>> right?
>> http://portal.open-bio.org/pipermail/bioperl-l/2005-December/ 
>> 020389.html
>>
>> The two first things to do is to check whether you run out of shared
>> memory and to run the tests and see whether the location where the
>> process gets killed can be narrowed down. If it's not a bug (which it
>> is unlikely to be - but the tests will provide more evidence) then the
>>  next step would be to recompile your own perl, DBI and DBD::Pg, and
>> PostgreSQL, in that order.
>>
>>         -hilmar
>>
>> On Dec 30, 2005, at 4:13 PM, Angshu Kar wrote:
>>
>> > oops! he is not present now!
>> > anyways, if you have some time could you please if there are any
>> > reasons for the script to get killed with the .gbk file?
>> >
>> > Thanks,
>> > Angshu
>> >
>> > On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
>> >> actually in a config file, and the default installation of Postgres
>> >> makes this config file unreadable for every one except the pg-admin
>> >> user chosen at installation time.
>> >>
>> >> -hilmar
>> >>
>> >> On Dec 30, 2005, at 3:15 PM, Angshu Kar wrote:
>> >>
>> >> > I've no clue about my Pg setup! It has been done by the  
>> sysadmin! :(
>> >> > Could you please tell me the commands and I can run and let you  
>> know
>> >> > the reports?
>> >> >
>> >> > thanks,
>> >> > angshu
>> >> >
>> >> > On 12/30/05, Hilmar Lapp <[hidden email]> wrote:
>> >> >>
>> >> >> Also, you haven't reported your hw setup. In particular, how  
>> much
>> >> >> memory and swap do you have, is Pg running locally (your command
>> >> line
>> >> >> suggests it does), and how much memory have you allocated to Pg?
>> >> >>
>> >> >> -hilmar
>> >> >>
>> >> >> On Dec 30, 2005, at 3:01 PM, Angshu Kar wrote:
>> >> >>
>> >> >> > Yes Hilmar its indeed a full sequence of chromosome. I got it
>> >> from
>> >> >> > ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
>> >> >> > I tried with the .faa and .fna files and they ran  
>> successfully.
>> >> >> > Also I missed a line (may be relevant) in the debug o/p:
>> >> >> > no adaptor found for class Bio::Annotation::TypeManager
>> >> >> >
>> >> >> > Thanks,
>> >> >> > Angshu
>> >> >> >
>> >> >> >
>> >> >> > On 12/30/05, Hilmar Lapp < [hidden email]> wrote:
>> >> >> >> special about this one? The file name lets me guess the input
>> >> is a
>> >> >> >> contig or even a full chromosome? Is the input on which the
>> >> process
>> >> >> >> wasn't killed of the same nature? Are the sequences of
>> >> comparable
>> >> >> or
>> >> >> >> vastly different lengths? Is there only a single contig in  
>> the
>> >> >> >> offending input? Can you reproduce the problem on an empty
>> >> database
>> >> >> >> with input containing a single entry? If so, let me know  
>> where I
>> >> >> can
>> >> >> >> get that file from and I'll try to reproduce it locally.
>> >> >> >>
>> >> >> >> -hilmar
>> >> >> >>
>> >> >> >> On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:
>> >> >> >>
>> >> >> >> > Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl
>> >> >> >> > --dbname=USBA --dbuser=postgres --format=genbank  
>> --driver=Pg
>> >> >> --debug
>> >> >> >> > NC_003076.gbk)
>> >> >> >> > is getting killed after the follwoing step?
>> >>  >> >> >
>> >> >> >> >Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as  
>> driver
>> >> peer
>> >> >> >> > for Bio::DB::BioSQL::BiosequenceAdaptor
>> >> >> >> > preparing SELECT statement: SELECT bioentry_id FROM
>> >> biosequence
>> >> >> >> WHERE
>> >> >> >> > bioentry_id = ?
>> >> >> >> >
>> >> >> >> > Killed
>> >> >> >> >
>> >> >> >> > I'm using a linux box. This didn't happen for a different  
>> i/p
>> >> >> file!
>> >> >> >> >
>> >> >> >> > Thanks,
>> >> >> >> > Angshu
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On 12/29/05, Angshu Kar < [hidden email]> wrote: I'm  
>> sorry
>> >> >> that
>> >> >> >> I
>> >> >> >> > missed it! Thanks for pointing it out.
>> >> >> >> >> Also thanks Hilmar for the update.
>> >> >> >> >>
>> >> >> >> >> Angshu
>> >> >> >> >>
>> >> >> >> >>
>> >> >>>> >> On 12/29/05, Torsten Seemann <
>> >> >> >> [hidden email]
>> >> >> >> >> > wrote:> I'm getting the following error while trying to
>> >> run :
>> >> >> >> >>> > ./load_seqdatabase.pl -host localhost -dbname USBA  
>> -dbuser
>> >> >> >> >>> postgres -format
>> >> >> >> >>> > genbank NC_003076.gbk
>> >> >> >> >>> > MSG: failed to open connection: Can't connect to local
>> >> MySQL
>> >> >> >> >>> server through
>> >> >> >> >>> > socket '/var/lib/mysql/mysql.sock' (2)
>> >> >> >> >>> > But I've a postgreSQL db and not a MySQL one...could
>> >> anyone
>> >> >> >> please
>> >> >>>> >>> guide me
>> >> >> >> >>> > troubleshoot this?
>> >> >> >> >>>
>> >> >> >> >>> Did you read the documentation for the  
>> load_seqdatabase.pl
>> >> >> script?
>> >> >> >> >>>
>>  >> >> >> >>> It's in the script itself!
>> >> >> >> >>>
>> >> >> >> >>> =item --driver $driver
>> >> >> >> >>> the DBI driver name for the RDBMS e.g., mysql, Pg, or  
>> Oracle
>> >> >> >> >>> [mysql]
>> >> >> >> >>>
>> >> >> >> >>> The default DBI driver is [mysql].
>> >> >> >> >>>
>> >> >> >> >>> I think you want the option "-driver Pg".
>> >> >> >> >>>
>> >> >> >>>>> --
>> >> >> >> >>> Torsten Seemann
>> >> >> >> >>> Victorian Bioinformatics Consortium, Monash University,
>> >> >> Australia
>> >> >> >> >>> http://www.vicbioinformatics.com/
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> --
>> >> >> >> -------------------------------------------------------------
>> >> >> >> Hilmar Lappemail: lapp at gnf.org
>> >> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> >> >> -------------------------------------------------------------
>> >> >> >>
>> >> >> >>
>> >> >> >
>> >> >> >
>> >> >> --
>> >> >> -------------------------------------------------------------
>> >> >> Hilmar Lappemail: lapp at gnf.org
>> >> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> >> -------------------------------------------------------------
>> >> >>
>> >> >>
>> >> >>
>> >> --
>> >> -------------------------------------------------------------
>> >> Hilmar Lappemail: lapp at gnf.org
>> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> -------------------------------------------------------------
>> >>
>> >>
>> >>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



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Re: error running load_seqdatabase.pl

Li Chen-2
In reply to this post by Angshu Kar
Based  on my limited experience perl/bioperl works
PERFECTLY under linux system but not under window XP.
I suggest you install another linux system on your
computer (dual OS) so that you don't  have to do so
many troubleshooting.  

Li  

--- Angshu Kar <[hidden email]> wrote:

> Hi Hilmar,
>
> All my tests failed for my WInXP m/c!I'm really at a
> fix!:(
> Do I need to uninstall bioperl-db, bioperl and even
> perl??? How to do that?
> Please guide.
> I'll be obliged if anyone with WinXp (not cygwin)
> provides his/her feedback
> ...
>
> Thanks,
> Angshu
>
> Microsoft (R) Program Maintenance Utility   Version
> 1.50
> Copyright (c) Microsoft Corp 1988-94. All rights
> reserved.
>
>         C:\Perl\bin\perl.exe
> "-MExtUtils::Command::MM" "-e" "test_harness(0,
> 'bl
> ib\lib', 'blib\arch')" t\01dbadaptor.t t\02species.t
> t\03simpleseq.t
> t\04swiss.t
>  t\05seqfeature.t t\06comment.t t\07dblink.t
> t\08genbank.t t\09fuzzy2.t
> t\10ense
> mbl.t t\11locuslink.t t\12ontology.t t\13remove.t
> t\14query.t t\15cluster.t
> t\01dbadaptor.....driver not set at
> t/DBTestHarness.pm line 106
>        
>
DBTestHarness::driver('DBTestHarness=HASH(0x235278)')
> called at
> t/DBTest
> Harness.pm line 204
>        
>
DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')

> called at
> t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness',
> 'biosql') called at
> t\01dbadaptor.t
> line 20
> t\01dbadaptor.....dubious
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-19
>         Failed 19/19 tests, 0.00% okay
> t\02species.......driver not set at
> t/DBTestHarness.pm line 106
>        
>
DBTestHarness::driver('DBTestHarness=HASH(0x235278)')
> called at
> t/DBTest
> Harness.pm line 204
>        
>
DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')

> called at
> t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness',
> 'biosql') called at
> t\02species.t li
> ne 18
> t\02species.......dubious
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-65
>         Failed 65/65 tests, 0.00% okay
> t\03simpleseq.....driver not set at
> t/DBTestHarness.pm line 106
>        
>
DBTestHarness::driver('DBTestHarness=HASH(0x235278)')
> called at
> t/DBTest
> Harness.pm line 204
>        
>
DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')

> called at
> t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness',
> 'biosql') called at
> t\03simpleseq.t
> line 19
> t\03simpleseq.....dubious
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-59
>         Failed 59/59 tests, 0.00% okay
> t\04swiss.........driver not set at
> t/DBTestHarness.pm line 106
>        
>
DBTestHarness::driver('DBTestHarness=HASH(0x235278)')
> called at
> t/DBTest
> Harness.pm line 204
>        
>
DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')

> called at
> t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness',
> 'biosql') called at t\04swiss.t
> line
>  20
> t\04swiss.........dubious
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-52
>         Failed 52/52 tests, 0.00% okay
> t\05seqfeature....driver not set at
> t/DBTestHarness.pm line 106
>        
>
DBTestHarness::driver('DBTestHarness=HASH(0x235278)')
> called at
> t/DBTest
> Harness.pm line 204
>        
>
DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')

> called at
> t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness',
> 'biosql') called at
> t\05seqfeature.t
>  line 19
> t\05seqfeature....dubious
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-48
>         Failed 48/48 tests, 0.00% okay
> t\06comment.......driver not set at
> t/DBTestHarness.pm line 106
>        
>
DBTestHarness::driver('DBTestHarness=HASH(0x235278)')
> called at
> t/DBTest
> Harness.pm line 204
>        
>
DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')

> called at
> t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness',
> 'biosql') called at
> t\06comment.t li
> ne 20
> t\06comment.......dubious
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-11
>         Failed 11/11 tests, 0.00% okay
> t\07dblink........driver not set at
> t/DBTestHarness.pm line 106
>        
>
DBTestHarness::driver('DBTestHarness=HASH(0x235278)')
> called at
> t/DBTest
> Harness.pm line 204
>        
>
DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')

> called at
> t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness',
> 'biosql') called at t\07dblink.t
> lin
> e 21
> t\07dblink........dubious
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-18
>         Failed 18/18 tests, 0.00% okay
> t\08genbank.......driver not set at
> t/DBTestHarness.pm line 106
>        
>
DBTestHarness::driver('DBTestHarness=HASH(0x235278)')
> called at
> t/DBTest
> Harness.pm line 204
>        
>
DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')

> called at
> t/DBT
> estHarness.pm line 94
>         DBTestHarness::new('DBTestHarness',
> 'biosql') called at
> t\08genbank.t li
> ne 21
> t\08genbank.......dubious
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-18
>         Failed 18/18 tests, 0.00% okay
> t\09fuzzy2........driver not set at
> t/DBTestHarness.pm line 106
>        
>
DBTestHarness::driver('DBTestHarness=HASH(0x235278)')
> called at
> t/DBTest
> Harness.pm line 204
>        
>
DBTestHarness::create_db('DBTestHarness=HASH(0x235278)')
> called at
> t/DBT
>
=== message truncated ===



       
               
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