[Bioperl-l] error running load_seqdatabase.pl

Hilmar Lapp hlapp at gmx.net
Fri Dec 30 22:58:00 EST 2005


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 <hlapp at gmx.net> 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 <hlapp at gmx.net> 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 <hlapp at gmx.net> 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 < hlapp at gmx.net> 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 < angshu96 at gmail.com> 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 <
>> >> >> >> torsten.seemann at infotech.monash.edu.au
>> >> >> >> >> > 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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