error uploading data to mysql db.

[raul petrin]

Hello all.
I'm trying to upload my files to mysql db using bp_seqfeature_load.pl but every time I get this message:
MSG: early_female:scaffold1:1_3166976  doesn't have a primary id

command:
bp_seqfeature_load.pl -c -f -v -d dbname file1.gff3 file2.gff3 file3.gff3 --user=usert --password=pwd

file1:
scaffold_1    Sequence    scaffold    1    3167015    .    .    .    ID=scaffold_1;Name=scaffold_1   
scaffold_10    Sequence    scaffold    1    1154401    .    .    .    ID=scaffold_10;Name=scaffold_10   
scaffold_100    Sequence    scaffold    1    115756    .    .    .    ID=scaffold_100;Name=scaffold_100

file2:
##gff-version 3                               
#sequence-region scaffold_1 1 50716                               
scaffold_1    Gaze    gene    588    3589    2089.21    +    .    ID=GSOIDG00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    mRNA    588    3589    2089.21    +    .    ID=GSOIDT00000001001;Name=GSOIDT00000001001;Parent=GSOIDG00000001001
scaffold_1    Gaze    CDS    588    738    105.48    +    0    Parent=GSOIDT00000001001;Name=GSOIDG00000001001

file3:
##gff-version 3                               
#sequence-region scaffold1 1 3167015                                           
scaffold1    early_female    microarray_oligo    1    3166976    .    .    .    ID=early_female:scaffold1:1_3166976
scaffold1    early_female    region    8    57    815.56    .    .    Parent=early_female:scaffold1:1_3166976
scaffold1    early_female    region    36    85    405.56    .    .    Parent=early_female:scaffold1:1_3166976
scaffold1    early_female    region    60    109    509.56    .    .    Parent=early_female:scaffold1:1_3166976

Thanks for the help.
Raul


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[Scott Cain-4]

Hello Raul,

First, an important point: "scaffold_1" does not equal "scaffold1", so  
that is going to cause you a problem.  That does not relate to the  
message you are getting though.

About the message: I have tried very hard with different permutations  
of the files given below, and have been unable to reproduce it.  What  
version of BioPerl are you using?

Scott


On Sep 4, 2009, at 10:37 AM, raul petrin wrote:

> Hello all.
> I'm trying to upload my files to mysql db using  
> bp_seqfeature_load.pl but every time I get this message:
> MSG: early_female:scaffold1:1_3166976  doesn't have a primary id
>
> command:
> bp_seqfeature_load.pl -c -f -v -d dbname file1.gff3 file2.gff3  
> file3.gff3 --user=usert --password=pwd
>
> file1:
> scaffold_1    Sequence    scaffold    1    3167015    .    .    .    
> ID=scaffold_1;Name=scaffold_1
> scaffold_10    Sequence    scaffold    1    
> 1154401    .    .    .    ID=scaffold_10;Name=scaffold_10
> scaffold_100    Sequence    scaffold    1    
> 115756    .    .    .    ID=scaffold_100;Name=scaffold_100
>
> file2:
> ##gff-version 3
> #sequence-region scaffold_1 1 50716
> scaffold_1    Gaze    gene    588    3589    2089.21    +    .    
> ID=GSOIDG00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    mRNA    588    3589    2089.21    +    .    
> ID=GSOIDT00000001001;Name=GSOIDT00000001001;Parent=GSOIDG00000001001
> scaffold_1    Gaze    CDS    588    738    105.48    +    0    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
>
> file3:
> ##gff-version 3
> #sequence-region scaffold1 1 3167015
> scaffold1    early_female    microarray_oligo    1    
> 3166976    .    .    .    ID=early_female:scaffold1:1_3166976
> scaffold1    early_female    region    8    57    
> 815.56    .    .    Parent=early_female:scaffold1:1_3166976
> scaffold1    early_female    region    36    85    
> 405.56    .    .    Parent=early_female:scaffold1:1_3166976
> scaffold1    early_female    region    60    109    
> 509.56    .    .    Parent=early_female:scaffold1:1_3166976
>
> Thanks for the help.
> Raul
>
> ------------------------------------------------------------------------------
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> focus on
> what you do best, core application coding. Discover what's new with
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-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research





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[Scott Cain-4]

Hi Raul,

Please keep your responses on the list.

I've tried with both the mysql and postgres adaptors with BioPerl 1.6  
and this works for me.  Can you please post a log of the commands  
you've executed and the output of each?

Thanks,
Scott


On Sep 4, 2009, at 11:12 AM, raul petrin wrote:

> Hello Scott.
> I'm using BioPerl-1.6.0
> Thanks
>
>
> On Fri, Sep 4, 2009 at 10:04 AM, Scott Cain <scott@...>  
> wrote:
> Hello Raul,
>
> First, an important point: "scaffold_1" does not equal "scaffold1",  
> so that is going to cause you a problem.  That does not relate to  
> the message you are getting though.
>
> About the message: I have tried very hard with different  
> permutations of the files given below, and have been unable to  
> reproduce it.  What version of BioPerl are you using?
>
> Scott
>
>
>
> On Sep 4, 2009, at 10:37 AM, raul petrin wrote:
>
> Hello all.
> I'm trying to upload my files to mysql db using  
> bp_seqfeature_load.pl but every time I get this message:
> MSG: early_female:scaffold1:1_3166976  doesn't have a primary id
>
> command:
> bp_seqfeature_load.pl -c -f -v -d dbname file1.gff3 file2.gff3  
> file3.gff3 --user=usert --password=pwd
>
> file1:
> scaffold_1    Sequence    scaffold    1    3167015    .    .    .    
> ID=scaffold_1;Name=scaffold_1
> scaffold_10    Sequence    scaffold    1    
> 1154401    .    .    .    ID=scaffold_10;Name=scaffold_10
> scaffold_100    Sequence    scaffold    1    
> 115756    .    .    .    ID=scaffold_100;Name=scaffold_100
>
> file2:
> ##gff-version 3
> #sequence-region scaffold_1 1 50716
> scaffold_1    Gaze    gene    588    3589    2089.21    +    .    
> ID=GSOIDG00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    mRNA    588    3589    2089.21    +    .    
> ID=GSOIDT00000001001;Name=GSOIDT00000001001;Parent=GSOIDG00000001001
> scaffold_1    Gaze    CDS    588    738    105.48    +    0    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
>
> file3:
> ##gff-version 3
> #sequence-region scaffold1 1 3167015
> scaffold1    early_female    microarray_oligo    1    
> 3166976    .    .    .    ID=early_female:scaffold1:1_3166976
> scaffold1    early_female    region    8    57    
> 815.56    .    .    Parent=early_female:scaffold1:1_3166976
> scaffold1    early_female    region    36    85    
> 405.56    .    .    Parent=early_female:scaffold1:1_3166976
> scaffold1    early_female    region    60    109    
> 509.56    .    .    Parent=early_female:scaffold1:1_3166976
>
> Thanks for the help.
> Raul
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
> 30-Day
> trial. Simplify your report design, integration and deployment - and  
> focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july_______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> -----------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>
>
>
>
>

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





------------------------------------------------------------------------------
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[raul petrin]

Hello Scott. This is part of my log.

...

                    6 Query	SELECT id FROM locationlist WHERE seqname='scaffold_1'
		    6 Query	INSERT INTO locationlist (seqname) VALUES ('scaffold_1')

		    6 Query	SELECT id FROM locationlist WHERE seqname='scaffold_10'
		    6 Query	INSERT INTO locationlist (seqname) VALUES ('scaffold_10')

...

                    6 Query	SELECT id FROM locationlist WHERE seqname='scaffold_998'

		    6 Query	INSERT INTO locationlist (seqname) VALUES ('scaffold_998')
		    6 Query	SELECT id FROM locationlist WHERE seqname='scaffold_999'
		    6 Query	INSERT INTO locationlist (seqname) VALUES ('scaffold_999')

		    6 Query	LOAD DATA LOCAL INFILE '/tmp/feature.11637' REPLACE INTO TABLE feature FIELDS OPTIONALLY ENCLOSED BY '\''
		    6 Query	LOAD DATA LOCAL INFILE '/tmp/name.11637' REPLACE INTO TABLE name FIELDS OPTIONALLY ENCLOSED BY '\''

		    6 Query	LOAD DATA LOCAL INFILE '/tmp/attribute.11637' REPLACE INTO TABLE attribute FIELDS OPTIONALLY ENCLOSED BY '\''
		    6 Query	LOAD DATA LOCAL INFILE '/tmp/parent2child.11637' REPLACE INTO TABLE parent2child FIELDS OPTIONALLY ENCLOSED BY '\''

		    6 Query	SELECT id FROM typelist WHERE tag='gene:Gaze'
		    6 Query	INSERT INTO typelist (tag) VALUES ('gene:Gaze')
		    6 Query	SELECT id FROM typelist WHERE tag='mRNA:Gaze'
		    6 Query	INSERT INTO typelist (tag) VALUES ('mRNA:Gaze')

		    6 Query	SELECT id FROM attributelist WHERE tag='parent_id'
		    6 Query	INSERT INTO attributelist (tag) VALUES ('parent_id')
		    6 Query	SELECT id FROM typelist WHERE tag='CDS:Gaze'

		    6 Query	INSERT INTO typelist (tag) VALUES ('CDS:Gaze')
		    6 Query	SELECT id FROM typelist WHERE tag='UTR:Gaze'
		    6 Query	INSERT INTO typelist (tag) VALUES ('UTR:Gaze')
		    6 Query	LOAD DATA LOCAL INFILE '/tmp/feature.11637' REPLACE INTO TABLE feature FIELDS OPTIONALLY ENCLOSED BY '\''

		    6 Query	LOAD DATA LOCAL INFILE '/tmp/name.11637' REPLACE INTO TABLE name FIELDS OPTIONALLY ENCLOSED BY '\''
		    6 Query	LOAD DATA LOCAL INFILE '/tmp/attribute.11637' REPLACE INTO TABLE attribute FIELDS OPTIONALLY ENCLOSED BY '\''

		    6 Query	LOAD DATA LOCAL INFILE '/tmp/parent2child.11637' REPLACE INTO TABLE parent2child FIELDS OPTIONALLY ENCLOSED BY '\''
		    6 Query	SELECT id FROM typelist WHERE tag='microarray_oligo:early_female'

		    6 Query	INSERT INTO typelist (tag) VALUES ('microarray_oligo:early_female')
		    6 Query	SELECT id FROM typelist WHERE tag='region:early_female'
		    6 Query	INSERT INTO typelist (tag) VALUES ('region:early_female')

090904 13:13:50	    6 Quit

mysql> select * from typelist;
+----+-------------------------------+
| id | tag                                       |
+----+-------------------------------+
|  1 | scaffold:Sequence                 |
|  2 | gene:Gaze                            |
|  3 | mRNA:Gaze                          |
|  4 | CDS:Gaze                             |
|  5 | UTR:Gaze                             |
|  6 | microarray_oligo:early_female |
|  7 | region:early_female                 |
+----+-------------------------------+
7 rows in set (0.00 sec

file1
scaffoldA_991    Sequence    scaffold    1    12491    .    .    .    ID=scaffoldA_991;Name=scaffoldA_991   
scaffoldA_992    Sequence    scaffold    1    12476    .    .    .    ID=scaffoldA_992;Name=scaffoldA_992   
scaffoldA_993    Sequence    scaffold    1    12441    .    .    .    ID=scaffoldA_993;Name=scaffoldA_993   
scaffoldA_994    Sequence    scaffold    1    12429    .    .    .    ID=scaffoldA_994;Name=scaffoldA_994   
scaffoldA_995    Sequence    scaffold    1    12424    .    .    .    ID=scaffoldA_995;Name=scaffoldA_995   
scaffoldA_996    Sequence    scaffold    1    12399    .    .    .    ID=scaffoldA_996;Name=scaffoldA_996   
scaffoldA_997    Sequence    scaffold    1    12392    .    .    .    ID=scaffoldA_997;Name=scaffoldA_997   
scaffoldA_998    Sequence    scaffold    1    12352    .    .    .    ID=scaffoldA_998;Name=scaffoldA_998   
scaffoldA_999    Sequence    scaffold    1    12345    .    .    .    ID=scaffoldA_999;Name=scaffoldA_999   
scaffold_1    Sequence    scaffold    1    3167015    .    .    .    ID=scaffold_1;Name=scaffold_1   
scaffold_10    Sequence    scaffold    1    1154401    .    .    .    ID=scaffold_10;Name=scaffold_10   
scaffold_100    Sequence    scaffold    1    115756    .    .    .    ID=scaffold_100;Name=scaffold_100   
scaffold_1000    Sequence    scaffold    1    3586    .    .    .    ID=scaffold_1000;Name=scaffold_1000   
scaffold_1001    Sequence    scaffold    1    3586    .    .    .    ID=scaffold_1001;Name=scaffold_1001   
scaffold_1002    Sequence    scaffold    1    3579    .    .    .    ID=scaffold_1002;Name=scaffold_1002   
scaffold_1003    Sequence    scaffold    1    3578    .    .    .    ID=scaffold_1003;Name=scaffold_1003   
scaffold_1004    Sequence    scaffold    1    3543    .    .    .    ID=scaffold_1004;Name=scaffold_1004   
scaffold_1005    Sequence    scaffold    1    3517    .    .    .    ID=scaffold_1005;Name=scaffold_1005   
scaffold_1006    Sequence    scaffold    1    3515    .    .    .    ID=scaffold_1006;Name=scaffold_1006   
scaffold_1007    Sequence    scaffold    1    3501    .    .    .    ID=scaffold_1007;Name=scaffold_1007   
scaffold_1008    Sequence    scaffold    1    3493    .    .    .    ID=scaffold_1008;Name=scaffold_1008   
scaffold_1009    Sequence    scaffold    1    3490    .    .    .    ID=scaffold_1009;Name=scaffold_1009   
scaffold_101    Sequence    scaffold    1    113812    .    .    .    ID=scaffold_101;Name=scaffold_101

file2
##gff-version 3                               
#sequence-region scaffold_1 1 50716                               
scaffold_1    Gaze    gene    588    3589    2089.21    +    .    ID=GSOIDG00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    mRNA    588    3589    2089.21    +    .    ID=GSOIDT00000001001;Name=GSOIDT00000001001;Parent=GSOIDG00000001001
scaffold_1    Gaze    CDS    588    738    105.48    +    0    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    811    922    74.4    +    1    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    1019    1086    80.33    +    2    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    1178    1337    73.33    +    1    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    1622    1662    38    +    2    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    1887    2089    141.92    +    1    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    2135    2217    151.07    +    0    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    2264    2623    124.32    +    2    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    2754    2981    80.82    +    2    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    3532    3589    1    +    2    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    gene    4545    6458    13.29    -    .    ID=GSOIDG00000002001;Name=GSOIDG00000002001
scaffold_1    Gaze    mRNA    4545    6458    13.29    -    .    ID=GSOIDT00000002001;Name=GSOIDT00000002001;Parent=GSOIDG00000002001

file3
##gff-version 3                               
#sequence-region scaffold_1 1 3167015                                           
scaffold_1    early_female    microarray_oligo    1    900    .    .    .    ID=early_female:scaffold_1:1_900
scaffold_1    early_female    region    8    57    815.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    36    85    405.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    60    109    509.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    85    134    356.89    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    122    171    579.22    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    145    194    1367.44    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    169    220    838.33    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    201    258    999.44    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    235    297    559.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    260    321    366.44    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    283    336    752.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    346    395    622.33    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    367    423    575.44    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    403    456    564    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    430    488    5957.11    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    449    513    457.33    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    482    541    616.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    515    574    1098.44    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    539    597    547.33    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    571    629    494    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    598    649    1126.89    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    618    673    1422.89    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    650    708    563.78    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    675    730    756.22    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    703    754    373.33    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    736    789    434.89    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    767    821    423    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    786    841    545.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    822    878    495    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    851    900    652.78    .    .    Parent=early_female:scaffold_1:1_900


error when I'm loading my files.

105781 features loaded in 54.28s                                                Building object tree...        
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: early_female:scaffold_1:1_3166976  doesn't have a primary id
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:357
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/GFF3Loader.pm:668
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/GFF3Loader.pm:647
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/GFF3Loader.pm:318
STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/Loader.pm:322
STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/Loader.pm:219
STACK: /usr/local/bin/bp_seqfeature_load.pl:102

Thanks
Raul

On Fri, Sep 4, 2009 at 10:34 AM, Scott Cain <scott@...> wrote:

Hi Raul,

Please keep your responses on the list.

I've tried with both the mysql and postgres adaptors with BioPerl 1.6 and this works for me.  Can you please post a log of the commands you've executed and the output of each?

Thanks,
Scott

On Sep 4, 2009, at 11:12 AM, raul petrin wrote:

Hello Scott.
I'm using BioPerl-1.6.0
Thanks


On Fri, Sep 4, 2009 at 10:04 AM, Scott Cain <scott@...> wrote:
Hello Raul,

First, an important point: "scaffold_1" does not equal "scaffold1", so that is going to cause you a problem.  That does not relate to the message you are getting though.

About the message: I have tried very hard with different permutations of the files given below, and have been unable to reproduce it.  What version of BioPerl are you using?

Scott



On Sep 4, 2009, at 10:37 AM, raul petrin wrote:

Hello all.
I'm trying to upload my files to mysql db using bp_seqfeature_load.pl but every time I get this message:
MSG: early_female:scaffold1:1_3166976  doesn't have a primary id

command:
bp_seqfeature_load.pl -c -f -v -d dbname file1.gff3 file2.gff3 file3.gff3 --user=usert --password=pwd

file1:
scaffold_1    Sequence    scaffold    1    3167015    .    .    .    ID=scaffold_1;Name=scaffold_1
scaffold_10    Sequence    scaffold    1    1154401    .    .    .    ID=scaffold_10;Name=scaffold_10
scaffold_100    Sequence    scaffold    1    115756    .    .    .    ID=scaffold_100;Name=scaffold_100

file2:
##gff-version 3
#sequence-region scaffold_1 1 50716
scaffold_1    Gaze    gene    588    3589    2089.21    +    .    ID=GSOIDG00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    mRNA    588    3589    2089.21    +    .    ID=GSOIDT00000001001;Name=GSOIDT00000001001;Parent=GSOIDG00000001001
scaffold_1    Gaze    CDS    588    738    105.48    +    0    Parent=GSOIDT00000001001;Name=GSOIDG00000001001

file3:
##gff-version 3
#sequence-region scaffold1 1 3167015
scaffold1    early_female    microarray_oligo    1    3166976    .    .    .    ID=early_female:scaffold1:1_3166976
scaffold1    early_female    region    8    57    815.56    .    .    Parent=early_female:scaffold1:1_3166976
scaffold1    early_female    region    36    85    405.56    .    .    Parent=early_female:scaffold1:1_3166976
scaffold1    early_female    region    60    109    509.56    .    .    Parent=early_female:scaffold1:1_3166976

Thanks for the help.
Raul

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[Scott Cain-4]

Hi Raul,

I have two suggestions:

1. Try updating to bioperl-live.  There were some database-related  
issues I fixed recently related to SFStore that may be affecting what  
you're trying to do.  See:

   http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN

(This will be not too different from 1.6.1, which will be released  
soon.)

2.  Create a small set of files that reproduce this bug and send them  
to the list so I can try to reproduce it.  Copying what you paste into  
an email to recreate it hasn't worked.

Thanks,
Scott

On Sep 4, 2009, at 2:27 PM, raul petrin wrote:

> Hello Scott. This is part of my log.
>
> ...
>                     6 Query SELECT id FROM locationlist WHERE  
> seqname='scaffold_1'
>    6 Query INSERT INTO locationlist (seqname) VALUES ('scaffold_1')
>
>    6 Query SELECT id FROM locationlist WHERE seqname='scaffold_10'
>    6 Query INSERT INTO locationlist (seqname) VALUES  
> ('scaffold_10')
> ...
>                     6 Query SELECT id FROM locationlist WHERE  
> seqname='scaffold_998'
>
>    6 Query INSERT INTO locationlist (seqname) VALUES  
> ('scaffold_998')
>    6 Query SELECT id FROM locationlist WHERE seqname='scaffold_999'
>    6 Query INSERT INTO locationlist (seqname) VALUES  
> ('scaffold_999')
>
>    6 Query LOAD DATA LOCAL INFILE '/tmp/feature.11637' REPLACE  
> INTO TABLE feature FIELDS OPTIONALLY ENCLOSED BY '\''
>    6 Query LOAD DATA LOCAL INFILE '/tmp/name.11637' REPLACE INTO  
> TABLE name FIELDS OPTIONALLY ENCLOSED BY '\''
>
>    6 Query LOAD DATA LOCAL INFILE '/tmp/attribute.11637' REPLACE  
> INTO TABLE attribute FIELDS OPTIONALLY ENCLOSED BY '\''
>    6 Query LOAD DATA LOCAL INFILE '/tmp/parent2child.11637'  
> REPLACE INTO TABLE parent2child FIELDS OPTIONALLY ENCLOSED BY '\''
>
>    6 Query SELECT id FROM typelist WHERE tag='gene:Gaze'
>    6 Query INSERT INTO typelist (tag) VALUES ('gene:Gaze')
>    6 Query SELECT id FROM typelist WHERE tag='mRNA:Gaze'
>    6 Query INSERT INTO typelist (tag) VALUES ('mRNA:Gaze')
>
>    6 Query SELECT id FROM attributelist WHERE tag='parent_id'
>    6 Query INSERT INTO attributelist (tag) VALUES ('parent_id')
>    6 Query SELECT id FROM typelist WHERE tag='CDS:Gaze'
>
>    6 Query INSERT INTO typelist (tag) VALUES ('CDS:Gaze')
>    6 Query SELECT id FROM typelist WHERE tag='UTR:Gaze'
>    6 Query INSERT INTO typelist (tag) VALUES ('UTR:Gaze')
>    6 Query LOAD DATA LOCAL INFILE '/tmp/feature.11637' REPLACE  
> INTO TABLE feature FIELDS OPTIONALLY ENCLOSED BY '\''
>
>    6 Query LOAD DATA LOCAL INFILE '/tmp/name.11637' REPLACE INTO  
> TABLE name FIELDS OPTIONALLY ENCLOSED BY '\''
>    6 Query LOAD DATA LOCAL INFILE '/tmp/attribute.11637' REPLACE  
> INTO TABLE attribute FIELDS OPTIONALLY ENCLOSED BY '\''
>
>    6 Query LOAD DATA LOCAL INFILE '/tmp/parent2child.11637'  
> REPLACE INTO TABLE parent2child FIELDS OPTIONALLY ENCLOSED BY '\''
>    6 Query SELECT id FROM typelist WHERE  
> tag='microarray_oligo:early_female'
>
>    6 Query INSERT INTO typelist (tag) VALUES  
> ('microarray_oligo:early_female')
>    6 Query SELECT id FROM typelist WHERE tag='region:early_female'
>    6 Query INSERT INTO typelist (tag) VALUES  
> ('region:early_female')
>
> 090904 13:13:50    6 Quit
>
> mysql> select * from typelist;
> +----+-------------------------------+
> | id | tag                                       |
> +----+-------------------------------+
> |  1 | scaffold:Sequence                 |
> |  2 | gene:Gaze                            |
> |  3 | mRNA:Gaze                          |
> |  4 | CDS:Gaze                             |
> |  5 | UTR:Gaze                             |
> |  6 | microarray_oligo:early_female |
> |  7 | region:early_female                 |
> +----+-------------------------------+
> 7 rows in set (0.00 sec
>
> file1
> scaffoldA_991    Sequence    scaffold    1    
> 12491    .    .    .    ID=scaffoldA_991;Name=scaffoldA_991
> scaffoldA_992    Sequence    scaffold    1    
> 12476    .    .    .    ID=scaffoldA_992;Name=scaffoldA_992
> scaffoldA_993    Sequence    scaffold    1    
> 12441    .    .    .    ID=scaffoldA_993;Name=scaffoldA_993
> scaffoldA_994    Sequence    scaffold    1    
> 12429    .    .    .    ID=scaffoldA_994;Name=scaffoldA_994
> scaffoldA_995    Sequence    scaffold    1    
> 12424    .    .    .    ID=scaffoldA_995;Name=scaffoldA_995
> scaffoldA_996    Sequence    scaffold    1    
> 12399    .    .    .    ID=scaffoldA_996;Name=scaffoldA_996
> scaffoldA_997    Sequence    scaffold    1    
> 12392    .    .    .    ID=scaffoldA_997;Name=scaffoldA_997
> scaffoldA_998    Sequence    scaffold    1    
> 12352    .    .    .    ID=scaffoldA_998;Name=scaffoldA_998
> scaffoldA_999    Sequence    scaffold    1    
> 12345    .    .    .    ID=scaffoldA_999;Name=scaffoldA_999
> scaffold_1    Sequence    scaffold    1    3167015    .    .    .    
> ID=scaffold_1;Name=scaffold_1
> scaffold_10    Sequence    scaffold    1    
> 1154401    .    .    .    ID=scaffold_10;Name=scaffold_10
> scaffold_100    Sequence    scaffold    1    
> 115756    .    .    .    ID=scaffold_100;Name=scaffold_100
> scaffold_1000    Sequence    scaffold    1    3586    .    .    .    
> ID=scaffold_1000;Name=scaffold_1000
> scaffold_1001    Sequence    scaffold    1    3586    .    .    .    
> ID=scaffold_1001;Name=scaffold_1001
> scaffold_1002    Sequence    scaffold    1    3579    .    .    .    
> ID=scaffold_1002;Name=scaffold_1002
> scaffold_1003    Sequence    scaffold    1    3578    .    .    .    
> ID=scaffold_1003;Name=scaffold_1003
> scaffold_1004    Sequence    scaffold    1    3543    .    .    .    
> ID=scaffold_1004;Name=scaffold_1004
> scaffold_1005    Sequence    scaffold    1    3517    .    .    .    
> ID=scaffold_1005;Name=scaffold_1005
> scaffold_1006    Sequence    scaffold    1    3515    .    .    .    
> ID=scaffold_1006;Name=scaffold_1006
> scaffold_1007    Sequence    scaffold    1    3501    .    .    .    
> ID=scaffold_1007;Name=scaffold_1007
> scaffold_1008    Sequence    scaffold    1    3493    .    .    .    
> ID=scaffold_1008;Name=scaffold_1008
> scaffold_1009    Sequence    scaffold    1    3490    .    .    .    
> ID=scaffold_1009;Name=scaffold_1009
> scaffold_101    Sequence    scaffold    1    
> 113812    .    .    .    ID=scaffold_101;Name=scaffold_101
>
> file2
> ##gff-version 3
> #sequence-region scaffold_1 1 50716
> scaffold_1    Gaze    gene    588    3589    2089.21    +    .    
> ID=GSOIDG00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    mRNA    588    3589    2089.21    +    .    
> ID=GSOIDT00000001001;Name=GSOIDT00000001001;Parent=GSOIDG00000001001
> scaffold_1    Gaze    CDS    588    738    105.48    +    0    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    CDS    811    922    74.4    +    1    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    CDS    1019    1086    80.33    +    2    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    CDS    1178    1337    73.33    +    1    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    CDS    1622    1662    38    +    2    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    CDS    1887    2089    141.92    +    1    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    CDS    2135    2217    151.07    +    0    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    CDS    2264    2623    124.32    +    2    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    CDS    2754    2981    80.82    +    2    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    CDS    3532    3589    1    +    2    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    gene    4545    6458    13.29    -    .    
> ID=GSOIDG00000002001;Name=GSOIDG00000002001
> scaffold_1    Gaze    mRNA    4545    6458    13.29    -    .    
> ID=GSOIDT00000002001;Name=GSOIDT00000002001;Parent=GSOIDG00000002001
>
> file3
> ##gff-version 3
> #sequence-region scaffold_1 1 3167015
> scaffold_1    early_female    microarray_oligo    1    
> 900    .    .    .    ID=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    8    57    
> 815.56    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    36    85    
> 405.56    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    60    109    
> 509.56    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    85    134    
> 356.89    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    122    171    
> 579.22    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    145    194    
> 1367.44    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    169    220    
> 838.33    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    201    258    
> 999.44    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    235    297    
> 559.56    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    260    321    
> 366.44    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    283    336    
> 752.56    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    346    395    
> 622.33    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    367    423    
> 575.44    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    403    456    
> 564    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    430    488    
> 5957.11    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    449    513    
> 457.33    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    482    541    
> 616.56    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    515    574    
> 1098.44    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    539    597    
> 547.33    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    571    629    
> 494    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    598    649    
> 1126.89    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    618    673    
> 1422.89    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    650    708    
> 563.78    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    675    730    
> 756.22    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    703    754    
> 373.33    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    736    789    
> 434.89    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    767    821    
> 423    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    786    841    
> 545.56    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    822    878    
> 495    .    .    Parent=early_female:scaffold_1:1_900
> scaffold_1    early_female    region    851    900    
> 652.78    .    .    Parent=early_female:scaffold_1:1_900
>
>
> error when I'm loading my files.
>
> 105781 features loaded in  
> 54.28s                                                Building  
> object tree...
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: early_female:scaffold_1:1_3166976  doesn't have a primary id
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.10.0/
> Bio/Root/Root.pm:357
> STACK:  
> Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /
> usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/
> GFF3Loader.pm:668
> STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /
> usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/
> GFF3Loader.pm:647
> STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/
> local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/
> GFF3Loader.pm:318
> STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/lib/
> perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/Loader.pm:322
> STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/lib/perl5/
> site_perl/5.10.0/Bio/DB/SeqFeature/Store/Loader.pm:219
> STACK: /usr/local/bin/bp_seqfeature_load.pl:102
>
> Thanks
> Raul
>
>
> On Fri, Sep 4, 2009 at 10:34 AM, Scott Cain <scott@...>  
> wrote:
> Hi Raul,
>
> Please keep your responses on the list.
>
> I've tried with both the mysql and postgres adaptors with BioPerl  
> 1.6 and this works for me.  Can you please post a log of the  
> commands you've executed and the output of each?
>
> Thanks,
> Scott
>
>
>
> On Sep 4, 2009, at 11:12 AM, raul petrin wrote:
>
> Hello Scott.
> I'm using BioPerl-1.6.0
> Thanks
>
>
> On Fri, Sep 4, 2009 at 10:04 AM, Scott Cain <scott@...>  
> wrote:
> Hello Raul,
>
> First, an important point: "scaffold_1" does not equal "scaffold1",  
> so that is going to cause you a problem.  That does not relate to  
> the message you are getting though.
>
> About the message: I have tried very hard with different  
> permutations of the files given below, and have been unable to  
> reproduce it.  What version of BioPerl are you using?
>
> Scott
>
>
>
> On Sep 4, 2009, at 10:37 AM, raul petrin wrote:
>
> Hello all.
> I'm trying to upload my files to mysql db using  
> bp_seqfeature_load.pl but every time I get this message:
> MSG: early_female:scaffold1:1_3166976  doesn't have a primary id
>
> command:
> bp_seqfeature_load.pl -c -f -v -d dbname file1.gff3 file2.gff3  
> file3.gff3 --user=usert --password=pwd
>
> file1:
> scaffold_1    Sequence    scaffold    1    3167015    .    .    .    
> ID=scaffold_1;Name=scaffold_1
> scaffold_10    Sequence    scaffold    1    
> 1154401    .    .    .    ID=scaffold_10;Name=scaffold_10
> scaffold_100    Sequence    scaffold    1    
> 115756    .    .    .    ID=scaffold_100;Name=scaffold_100
>
> file2:
> ##gff-version 3
> #sequence-region scaffold_1 1 50716
> scaffold_1    Gaze    gene    588    3589    2089.21    +    .    
> ID=GSOIDG00000001001;Name=GSOIDG00000001001
> scaffold_1    Gaze    mRNA    588    3589    2089.21    +    .    
> ID=GSOIDT00000001001;Name=GSOIDT00000001001;Parent=GSOIDG00000001001
> scaffold_1    Gaze    CDS    588    738    105.48    +    0    
> Parent=GSOIDT00000001001;Name=GSOIDG00000001001
>
> file3:
> ##gff-version 3
> #sequence-region scaffold1 1 3167015
> scaffold1    early_female    microarray_oligo    1    
> 3166976    .    .    .    ID=early_female:scaffold1:1_3166976
> scaffold1    early_female    region    8    57    
> 815.56    .    .    Parent=early_female:scaffold1:1_3166976
> scaffold1    early_female    region    36    85    
> 405.56    .    .    Parent=early_female:scaffold1:1_3166976
> scaffold1    early_female    region    60    109    
> 509.56    .    .    Parent=early_female:scaffold1:1_3166976
>
> Thanks for the help.
> Raul
>
> ------------------------------------------------------------------------------
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> Ontario Institute for Cancer Research
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> -----------------------------------------------------------------------
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> Ontario Institute for Cancer Research
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Ontario Institute for Cancer Research





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[raul petrin]

Hello again Scott
Thanks
these 3 files are part of my original file.
I tried to load using these 3 files and I got the same message. I'll check bioperl-live.

[root@localhost]# bp_seqfeature_load.pl -c -f -v -d test file1.gff3 file2.gff3 file3.gff3 --user=user --password=pwd
loading file1.gff3...
52 features loaded in  0.07s                                                    Building object tree... 0.00s
Loading bulk data into database... 0.00s
load time:  0.08s
loading file2.gff3...
86 features loaded in  0.05s                                                    Building object tree... 0.00s
Loading bulk data into database... 0.01s
load time:  0.15s
loading file3.gff3...
31 features loaded in  0.02s                                                    Building object tree...    
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: early_female:scaffold_1:1_900  doesn't have a primary id
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:357
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/GFF3Loader.pm:668
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/GFF3Loader.pm:647
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/GFF3Loader.pm:318
STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/Loader.pm:322
STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/Loader.pm:219
STACK: /usr/local/bin/bp_seqfeature_load.pl:102

On Fri, Sep 4, 2009 at 1:50 PM, Scott Cain <scott@...> wrote:

Hi Raul,

I have two suggestions:

1. Try updating to bioperl-live.  There were some database-related issues I fixed recently related to SFStore that may be affecting what you're trying to do.  See:

 http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN

(This will be not too different from 1.6.1, which will be released soon.)

2.  Create a small set of files that reproduce this bug and send them to the list so I can try to reproduce it.  Copying what you paste into an email to recreate it hasn't worked.

Thanks,
Scott

On Sep 4, 2009, at 2:27 PM, raul petrin wrote:

Hello Scott. This is part of my log.

...
                   6 Query     SELECT id FROM locationlist WHERE seqname='scaffold_1'
                   6 Query     INSERT INTO locationlist (seqname) VALUES ('scaffold_1')

                   6 Query     SELECT id FROM locationlist WHERE seqname='scaffold_10'
                   6 Query     INSERT INTO locationlist (seqname) VALUES ('scaffold_10')
...
                   6 Query     SELECT id FROM locationlist WHERE seqname='scaffold_998'

                   6 Query     INSERT INTO locationlist (seqname) VALUES ('scaffold_998')
                   6 Query     SELECT id FROM locationlist WHERE seqname='scaffold_999'
                   6 Query     INSERT INTO locationlist (seqname) VALUES ('scaffold_999')

                   6 Query     LOAD DATA LOCAL INFILE '/tmp/feature.11637' REPLACE INTO TABLE feature FIELDS OPTIONALLY ENCLOSED BY '\''
                   6 Query     LOAD DATA LOCAL INFILE '/tmp/name.11637' REPLACE INTO TABLE name FIELDS OPTIONALLY ENCLOSED BY '\''

                   6 Query     LOAD DATA LOCAL INFILE '/tmp/attribute.11637' REPLACE INTO TABLE attribute FIELDS OPTIONALLY ENCLOSED BY '\''
                   6 Query     LOAD DATA LOCAL INFILE '/tmp/parent2child.11637' REPLACE INTO TABLE parent2child FIELDS OPTIONALLY ENCLOSED BY '\''

                   6 Query     SELECT id FROM typelist WHERE tag='gene:Gaze'
                   6 Query     INSERT INTO typelist (tag) VALUES ('gene:Gaze')
                   6 Query     SELECT id FROM typelist WHERE tag='mRNA:Gaze'
                   6 Query     INSERT INTO typelist (tag) VALUES ('mRNA:Gaze')

                   6 Query     SELECT id FROM attributelist WHERE tag='parent_id'
                   6 Query     INSERT INTO attributelist (tag) VALUES ('parent_id')
                   6 Query     SELECT id FROM typelist WHERE tag='CDS:Gaze'

                   6 Query     INSERT INTO typelist (tag) VALUES ('CDS:Gaze')
                   6 Query     SELECT id FROM typelist WHERE tag='UTR:Gaze'
                   6 Query     INSERT INTO typelist (tag) VALUES ('UTR:Gaze')
                   6 Query     LOAD DATA LOCAL INFILE '/tmp/feature.11637' REPLACE INTO TABLE feature FIELDS OPTIONALLY ENCLOSED BY '\''

                   6 Query     LOAD DATA LOCAL INFILE '/tmp/name.11637' REPLACE INTO TABLE name FIELDS OPTIONALLY ENCLOSED BY '\''
                   6 Query     LOAD DATA LOCAL INFILE '/tmp/attribute.11637' REPLACE INTO TABLE attribute FIELDS OPTIONALLY ENCLOSED BY '\''

                   6 Query     LOAD DATA LOCAL INFILE '/tmp/parent2child.11637' REPLACE INTO TABLE parent2child FIELDS OPTIONALLY ENCLOSED BY '\''
                   6 Query     SELECT id FROM typelist WHERE tag='microarray_oligo:early_female'

                   6 Query     INSERT INTO typelist (tag) VALUES ('microarray_oligo:early_female')
                   6 Query     SELECT id FROM typelist WHERE tag='region:early_female'
                   6 Query     INSERT INTO typelist (tag) VALUES ('region:early_female')

090904 13:13:50     6 Quit

mysql> select * from typelist;
+----+-------------------------------+
| id | tag                                       |
+----+-------------------------------+
|  1 | scaffold:Sequence                 |
|  2 | gene:Gaze                            |
|  3 | mRNA:Gaze                          |
|  4 | CDS:Gaze                             |
|  5 | UTR:Gaze                             |
|  6 | microarray_oligo:early_female |
|  7 | region:early_female                 |
+----+-------------------------------+
7 rows in set (0.00 sec

file1
scaffoldA_991    Sequence    scaffold    1    12491    .    .    .    ID=scaffoldA_991;Name=scaffoldA_991
scaffoldA_992    Sequence    scaffold    1    12476    .    .    .    ID=scaffoldA_992;Name=scaffoldA_992
scaffoldA_993    Sequence    scaffold    1    12441    .    .    .    ID=scaffoldA_993;Name=scaffoldA_993
scaffoldA_994    Sequence    scaffold    1    12429    .    .    .    ID=scaffoldA_994;Name=scaffoldA_994
scaffoldA_995    Sequence    scaffold    1    12424    .    .    .    ID=scaffoldA_995;Name=scaffoldA_995
scaffoldA_996    Sequence    scaffold    1    12399    .    .    .    ID=scaffoldA_996;Name=scaffoldA_996
scaffoldA_997    Sequence    scaffold    1    12392    .    .    .    ID=scaffoldA_997;Name=scaffoldA_997
scaffoldA_998    Sequence    scaffold    1    12352    .    .    .    ID=scaffoldA_998;Name=scaffoldA_998
scaffoldA_999    Sequence    scaffold    1    12345    .    .    .    ID=scaffoldA_999;Name=scaffoldA_999
scaffold_1    Sequence    scaffold    1    3167015    .    .    .    ID=scaffold_1;Name=scaffold_1
scaffold_10    Sequence    scaffold    1    1154401    .    .    .    ID=scaffold_10;Name=scaffold_10
scaffold_100    Sequence    scaffold    1    115756    .    .    .    ID=scaffold_100;Name=scaffold_100
scaffold_1000    Sequence    scaffold    1    3586    .    .    .    ID=scaffold_1000;Name=scaffold_1000
scaffold_1001    Sequence    scaffold    1    3586    .    .    .    ID=scaffold_1001;Name=scaffold_1001
scaffold_1002    Sequence    scaffold    1    3579    .    .    .    ID=scaffold_1002;Name=scaffold_1002
scaffold_1003    Sequence    scaffold    1    3578    .    .    .    ID=scaffold_1003;Name=scaffold_1003
scaffold_1004    Sequence    scaffold    1    3543    .    .    .    ID=scaffold_1004;Name=scaffold_1004
scaffold_1005    Sequence    scaffold    1    3517    .    .    .    ID=scaffold_1005;Name=scaffold_1005
scaffold_1006    Sequence    scaffold    1    3515    .    .    .    ID=scaffold_1006;Name=scaffold_1006
scaffold_1007    Sequence    scaffold    1    3501    .    .    .    ID=scaffold_1007;Name=scaffold_1007
scaffold_1008    Sequence    scaffold    1    3493    .    .    .    ID=scaffold_1008;Name=scaffold_1008
scaffold_1009    Sequence    scaffold    1    3490    .    .    .    ID=scaffold_1009;Name=scaffold_1009
scaffold_101    Sequence    scaffold    1    113812    .    .    .    ID=scaffold_101;Name=scaffold_101

file2
##gff-version 3
#sequence-region scaffold_1 1 50716
scaffold_1    Gaze    gene    588    3589    2089.21    +    .    ID=GSOIDG00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    mRNA    588    3589    2089.21    +    .    ID=GSOIDT00000001001;Name=GSOIDT00000001001;Parent=GSOIDG00000001001
scaffold_1    Gaze    CDS    588    738    105.48    +    0    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    811    922    74.4    +    1    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    1019    1086    80.33    +    2    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    1178    1337    73.33    +    1    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    1622    1662    38    +    2    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    1887    2089    141.92    +    1    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    2135    2217    151.07    +    0    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    2264    2623    124.32    +    2    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    2754    2981    80.82    +    2    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    CDS    3532    3589    1    +    2    Parent=GSOIDT00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    gene    4545    6458    13.29    -    .    ID=GSOIDG00000002001;Name=GSOIDG00000002001
scaffold_1    Gaze    mRNA    4545    6458    13.29    -    .    ID=GSOIDT00000002001;Name=GSOIDT00000002001;Parent=GSOIDG00000002001

file3
##gff-version 3
#sequence-region scaffold_1 1 3167015
scaffold_1    early_female    microarray_oligo    1    900    .    .    .    ID=early_female:scaffold_1:1_900
scaffold_1    early_female    region    8    57    815.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    36    85    405.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    60    109    509.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    85    134    356.89    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    122    171    579.22    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    145    194    1367.44    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    169    220    838.33    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    201    258    999.44    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    235    297    559.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    260    321    366.44    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    283    336    752.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    346    395    622.33    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    367    423    575.44    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    403    456    564    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    430    488    5957.11    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    449    513    457.33    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    482    541    616.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    515    574    1098.44    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    539    597    547.33    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    571    629    494    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    598    649    1126.89    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    618    673    1422.89    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    650    708    563.78    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    675    730    756.22    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    703    754    373.33    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    736    789    434.89    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    767    821    423    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    786    841    545.56    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    822    878    495    .    .    Parent=early_female:scaffold_1:1_900
scaffold_1    early_female    region    851    900    652.78    .    .    Parent=early_female:scaffold_1:1_900


error when I'm loading my files.

105781 features loaded in 54.28s                                                Building object tree...
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: early_female:scaffold_1:1_3166976  doesn't have a primary id
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:357
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/GFF3Loader.pm:668
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/GFF3Loader.pm:647
STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/GFF3Loader.pm:318
STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/Loader.pm:322
STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store/Loader.pm:219
STACK: /usr/local/bin/bp_seqfeature_load.pl:102

Thanks
Raul


On Fri, Sep 4, 2009 at 10:34 AM, Scott Cain <scott@...> wrote:
Hi Raul,

Please keep your responses on the list.

I've tried with both the mysql and postgres adaptors with BioPerl 1.6 and this works for me.  Can you please post a log of the commands you've executed and the output of each?

Thanks,
Scott



On Sep 4, 2009, at 11:12 AM, raul petrin wrote:

Hello Scott.
I'm using BioPerl-1.6.0
Thanks


On Fri, Sep 4, 2009 at 10:04 AM, Scott Cain <scott@...> wrote:
Hello Raul,

First, an important point: "scaffold_1" does not equal "scaffold1", so that is going to cause you a problem.  That does not relate to the message you are getting though.

About the message: I have tried very hard with different permutations of the files given below, and have been unable to reproduce it.  What version of BioPerl are you using?

Scott



On Sep 4, 2009, at 10:37 AM, raul petrin wrote:

Hello all.
I'm trying to upload my files to mysql db using bp_seqfeature_load.pl but every time I get this message:
MSG: early_female:scaffold1:1_3166976  doesn't have a primary id

command:
bp_seqfeature_load.pl -c -f -v -d dbname file1.gff3 file2.gff3 file3.gff3 --user=usert --password=pwd

file1:
scaffold_1    Sequence    scaffold    1    3167015    .    .    .    ID=scaffold_1;Name=scaffold_1
scaffold_10    Sequence    scaffold    1    1154401    .    .    .    ID=scaffold_10;Name=scaffold_10
scaffold_100    Sequence    scaffold    1    115756    .    .    .    ID=scaffold_100;Name=scaffold_100

file2:
##gff-version 3
#sequence-region scaffold_1 1 50716
scaffold_1    Gaze    gene    588    3589    2089.21    +    .    ID=GSOIDG00000001001;Name=GSOIDG00000001001
scaffold_1    Gaze    mRNA    588    3589    2089.21    +    .    ID=GSOIDT00000001001;Name=GSOIDT00000001001;Parent=GSOIDG00000001001
scaffold_1    Gaze    CDS    588    738    105.48    +    0    Parent=GSOIDT00000001001;Name=GSOIDG00000001001

file3:
##gff-version 3
#sequence-region scaffold1 1 3167015
scaffold1    early_female    microarray_oligo    1    3166976    .    .    .    ID=early_female:scaffold1:1_3166976
scaffold1    early_female    region    8    57    815.56    .    .    Parent=early_female:scaffold1:1_3166976
scaffold1    early_female    region    36    85    405.56    .    .    Parent=early_female:scaffold1:1_3166976
scaffold1    early_female    region    60    109    509.56    .    .    Parent=early_female:scaffold1:1_3166976

Thanks for the help.
Raul

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Ontario Institute for Cancer Research






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





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GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

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