[Bioperl-l] error running load_seqdatabase.pl
Hilmar Lapp
hlapp at gmx.net
Sat Dec 31 00:46:50 EST 2005
That's only the statistics - lacking any error messages what do you
expect me to glean from it?
On Dec 30, 2005, at 8:13 PM, Angshu Kar wrote:
> :) I'm sorry again.
> After setting the DBHarness I get the following from nmake test:
>
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-160
> Failed 158/160 tests, 1.25% okay
> Failed Test Stat Wstat Total Fail Failed List of Failed
> -----------------------------------------------------------------------
> ------
> t\01dbadaptor.t 5 1280 19 30 157.89% 5-19
> t\02species.t 255 65280 65 126 193.85% 3-65
> t\03simpleseq.t 5 1280 59 108 183.05% 6-59
> t\04swiss.t 255 65280 52 100 192.31% 3-52
> t\05seqfeature.t 255 65280 48 92 191.67% 3-48
> t\06comment.t 255 65280 11 18 163.64% 3-11
> t\07dblink.t 255 65280 18 32 177.78% 3-18
> t\08genbank.t 255 65280 18 32 177.78% 3-18
> t\09fuzzy2.t 255 65280 21 38 180.95% 3-21
> t\10ensembl.t 255 65280 15 26 173.33% 3-15
> t\11locuslink.t 255 65280 110 214 194.55% 4-110
> t\12ontology.t 9 2304 738 1470 199.19% 4-738
> t\13remove.t 255 65280 59 116 196.61% 2-59
> t\15cluster.t 255 65280 160 316 197.50% 3-160
> Failed 14/15 test scripts, 6.67% okay. 1359/1411 subtests failed,
> 3.69% okay.
> NMAKE : fatal error U1077: 'C:\WINDOWS\system32\cmd.exe' : return code
> '0xff'
> Stop.
>
> On 12/30/05, Hilmar Lapp <hlapp at gmx.net > wrote: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 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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