[Bioperl-l] Bioperl-DB error

Thu Mar 4 15:16:37 EST 2004

Hi Hilmar,

I would appreciate help on the following.  Previously, I had errors with the
make tests of both Bioperl-DB And Bioperl-1.4.  I went to CVS bioperl-live
and dowloaded again the Head branch of bioperl-db and bioperl-schema. As
well from bioperl-live I downloaded the bioperl-1.4 from branch 1.4. 

I have bioperl installed in two places.  I think it should be okay since the
Errors that I am receiving have reduced.  I not sure how to get rid of the
initial install or if it matters.

1) When I performed the make test for bioperl-db all of the tests passed but
there seems to be one warning and I am concerned That this will affect what
I want to do which is to load unigene information into the annotation
database that I am creating With the perl script load_seqdatabase.pl. Should
I be concerned about this warning?

[root@ bioperl-db]# make test PERL_DL_NONLAZY=1 /usr/bin/perl
"-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')"
t/*.t t/cluster.......

t/cluster.......ok 1/160

t/cluster.......ok 2/160

t/cluster.......ok 3/160

t/cluster.......ok 4/160

t/cluster.......ok 5/160

t/cluster.......ok 6/160

t/cluster.......ok 7/160

etc...

t/cluster.......ok 154/160

t/cluster.......ok 155/160
-------------------- WARNING ---------------------
MSG: failed to store one or more child objects for an instance of class
Bio::Cluster::UniGene (PK=1)
---------------------------------------------------

t/cluster.......ok 160/160

t/cluster.......ok
t/comment.......

All tests successful.
Files=15, Tests=930, 93 wallclock secs (31.64 cusr +  1.26 csys = 32.90 CPU)

2) I started with an empty database and I loaded the NCBI taxonomy into the
database, then the GO information then locuslink (I used
The --safe and --lookup options and did not get any errors).  Loading
locuslink information to half a day to a day.

Next I loaded unigene information and it is taking three days and is still
not finished?! (I meant to use the option --mergeobjs but forgot when I ran
the script but I don't think that this will make a difference in terms of
execution time) Something strange that is happening is that when I use
mysqlcc to refresh what the current state of the database is the number of
bioentries increases and then decreases.  However the general overall trend
is that the number of bioentries is increasing. Is this correct or is
something wrong happening.
I am wondering if loading of unigene information is affected by the warning
I got from the make test in bioperl-db
MSG: failed to store one or more child objects for an instance of class
Bio::Cluster::UniGene (PK=1).  If so, I am not sure how to
Resolve the problem.

3) On a related note every time including the initial time that I load the
database with load_ontology.pl, or load_seqdatbase.pl I use the option
lookup.  I want to create annotation database so I am loading first with
NCBI taxonomy databse, then GO, then locuslink, then unigene.  I want find
out the annotation for some clones from ESTs.  I think I only need to use
the mergobjs option when I load the unigene information?
I read the documentation of mergobjs in the load_seqdatbase.pl script but
would appreciate an example of how this works.

4) Also after I intalled Bioperl-1.4 again I decreased the number of failed
tests but still there Where 3 test failures and I am not sure if I should be
concerned about these.

t/AlignIO....................ok 75/80Bio::AlignIO: largemultifasta cannot be
found Exception 
------------- EXCEPTION  -------------
MSG: Failed to load module Bio::AlignIO::largemultifasta. Can't locate
Bio/Seq/LargeLocatableSeq.pm in @INC (@INC contains: t
/usr/lib/bioperl-live/blib/lib /usr/lib/bioperl-live/blib/arch
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
/usr/lib/bioperl-live/blib/lib/Bio/AlignIO/largemultifasta.pm line 69,
<GEN32> line 28. BEGIN failed--compilation aborted at
/usr/lib/bioperl-live/blib/lib/Bio/AlignIO/largemultifasta.pm line 69,
<GEN32> line 28. Compilation failed in require at
/usr/lib/bioperl-live/blib/lib/Bio/Root/Root.pm line 394, <GEN32> line 28.

STACK Bio::Root::Root::_load_module
/usr/lib/bioperl-live/blib/lib/Bio/Root/Root.pm:396
STACK (eval) /usr/lib/bioperl-live/blib/lib/Bio/AlignIO.pm:420
STACK Bio::AlignIO::_load_format_module
/usr/lib/bioperl-live/blib/lib/Bio/AlignIO.pm:419
STACK Bio::AlignIO::new /usr/lib/bioperl-live/blib/lib/Bio/AlignIO.pm:347
STACK toplevel t/AlignIO.t:283

--------------------------------------

For more information about the AlignIO system please see the AlignIO docs.
This includes ways of checking for formats at compile time, not run time
Can't call method "next_aln" on an undefined value at t/AlignIO.t line 285,
<GEN32> line 28.

t/AlignIO....................dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 76-80
	Failed 5/80 tests, 93.75% okay
t/AlignStats.................

-the other error I got was

t/GeneCoordinateMap
per.......ok 70/113

t/GeneCoordinateMapper.......ok 71/113
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define
seq_id (at least one sublocation does!)
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define
seq_id (at least one sublocation does!)
---------------------------------------------------

t/GeneCoordinateMapper.......ok 72/113

t/GeneCoordinateMapper.......ok 73/113

t/GeneCoordinateMapper.......ok 74/113

---the next error was

t/tutorial...................ok 9/21

t/tutorial...................ok 10/21
------------- EXCEPTION  -------------
MSG: WebDBSeqI Request Error:
HTTP/1.1 500 Internal Server Error
Connection: close
Date: Mon, 23 Feb 2004 15:59:50 GMT
Via: 1.1 eutils.ncbi.nih.gov
Server: Apache
Content-Type: text/html
Client-Date: Mon, 23 Feb 2004 16:05:33 GMT
Client-Response-Num: 1
Client-Transfer-Encoding: chunked
X-Cache: MISS from eutils.ncbi.nih.gov

<HTML>
<HEADER>
<TITLE>NCBI/xpubmed3 - WWW Error 500 Diagnostic</TITLE> </HEADER> <BODY>
<H1>Server Error</H1>

Your request could not be processed due to a problem on
our Web server. This could be a transient problem, please
try the query again. If it doesn't clear up within a reasonable period of
time, e-mail a short description of your query and the diagnostic
information shown below to: <CENTER><DT>pubmed at nlm.nih.gov - for
problems with PubMed info at ncbi.nlm.nih.gov - for problems with other
services </CENTER> Thank you for your assistance. We will try to
fix the problem as soon as possible. <HR> Diagnostic Information: <UL>
<DT>Error: 500

<DT>URL:
http://eutils.ncbi.nlm.nih.gov/entrez/viewer.fcgi?WebEnvRq=1&save=efetch&db=
nucleotide&val=gb%7CAF303112&retmode=text&dopt=gb&tmpl=__reset&tool=bioperl&
usehistory=n

<DT>User agent: bioperl-Bio_DB_GenBank/1.4

<DT>Client: 130.14.29.13

<DT>Server: xpubmed3

<DT>Time: Mon Feb 23 11:00:20 EST 2004

</UL>

NOTE: The above is an internal URL which may differ from the one you used to
address the page. <HR> Rev. 05/09/00

</BODY>
</HTML>

STACK Bio::DB::WebDBSeqI::_stream_request Bio/DB/WebDBSeqI.pm:728 STACK
Bio::DB::WebDBSeqI::get_seq_stream Bio/DB/WebDBSeqI.pm:460 STACK
Bio::DB::NCBIHelper::get_Stream_by_acc Bio/DB/NCBIHelper.pm:415 STACK
Bio::DB::WebDBSeqI::get_Seq_by_acc Bio/DB/WebDBSeqI.pm:181 STACK
Bio::DB::GenBank::get_Seq_by_acc Bio/DB/GenBank.pm:216 STACK main::__ANON__
/usr/lib/bioperl-live/blib/lib/bptutorial.pl:2920
STACK main::run_examples /usr/lib/bioperl-live/blib/lib/bptutorial.pl:4144
STACK toplevel t/tutorial.t:23

--------------------------------------

-------------------- WARNING ---------------------
MSG: acc (gb|AF303112) does not exist
---------------------------------------------------
Can't call method "display_id" on an undefined value at
/usr/lib/bioperl-live/blib/lib/bptutorial.pl line 2921.

t/tutorial...................dubious
	Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 11-21
	Failed 11/21 tests, 47.62% okay

Failed Test  Stat Wstat Total Fail  Failed  List of Failed
----------------------------------------------------------------------------
---
t/AlignIO.t     2   512    80    5   6.25%  76-80
t/DB.t                     78   ??       %  ??
t/tutorial.t  255 65280    21   11  52.38%  11-21
122 subtests skipped.
Failed 3/180 test scripts, 98.33% okay. 7/8305 subtests failed, 99.92% okay.

5) I have been loading the database with the following command. I would like
to know if the format option should be SeqIO:locuslink or should it simply
be locuslink? 

Perl /root/bioperl-db/scripts/biosql/load_seqdatabase.pl --dbuser=root
--dbpass=ms22a --dbname=annotatedata --namespace LocusLink 
--format SeqIO::locuslink /var/lib/mysql/LL_tmpl

thanks very much,
Annie.