[Gmod-help] Re: [Gmod-gbrowse] can't load to database

[Mao Mao]

Hi,

The GFF3 files were generated by the included wiggle2bed.pl perl program
from some wig files I had created using another perl program I wrote that
processed some experimental sequence data. The thing is, the hg18 database
isn't changed at all. In all the tables except the feature table, the tables
remain the same: no new entries in the attribute, attributelist, or feature
table: all contain exactly 49 entries (or 4 for meta table and 1 for
typelist) which I'm pretty sure is from my original human genome upload.

No matter how many times the bp_seqfeature.load.pl program runs, the hg18
database refuses to change; all tables contain the exact same entries, and
same number of entries as before.

I attached the exact c_389.pl file I tried to upload (I also tried it for
bunch of other gff3 files from other wig track files I had: no worked).

-Sincerely,
Mao


On Tue, Dec 16, 2008 at 4:03 PM, Dave Clements, GMOD Help Desk <
gmodhelp at googlemail.com> wrote:

> Hi Mao,
>
> Can you send me a pointer to where you got your GFF3 files for the
> human genome, and a copy of the c_389.gff3 file?
>
> It certainly appears that bp_seqfeature_load.pl thinks it loaded 41
> features.  Did the # of records in the feature table change at all as
> a result of the c_389.gff3 load?
>
> Thanks,
>
> Dave C.
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>
>
> On Thu, Dec 11, 2008 at 4:43 PM, Mao Mao <themao at gmail.com> wrote:
> > Hi,
> >
> > I recently deleted and recreated a hg18 mysql database to hold my data.
> > After I successfully uploaded the hg18 genome, I can get the
> > bp_seqfeature_load.pl program to work anymore. I haven't changed the perl
> > program, and when I use it I get all normal messages and no error
> messages
> > such as below:
> > [gmao at pipeline Chimp HpaII]$ bp_seqfeature_load.pl -f -d hg18 c_389.gff3
> > loading c_389.gff3...
> > 41 features loaded in
> > 0.00s                                                   Building object
> > tree... 0.00s
> > Loading bulk data into database... 0.00s
> > load time:  0.07s
> >
> > However, the hg18 mysql database isn't updated at all. I've looked
> through
> > all the tables (except feature and sequence) and nothing new was
> inserted.
> > The only thing in my database so far is the human genome, but none of the
> > tracks have managed to succesfully register into the database. I don't
> get
> > any typical error messages that might come from permission denied
> reasons:
> > [gmao at pipeline Chimp HpaII]$ bp_seqfeature_load.pl -f -d hg28 c_389.gff3
> > DBI connect('hg28','',...) failed: Access denied for user ''@'localhost'
> to
> > database 'hg28' at
> > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm line
> 211
> >
> > -------------------- EXCEPTION --------------------
> > MSG: Access denied for user ''@'localhost' to database 'hg28'
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::init
> > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/mysql.pm:211
> > STACK Bio::DB::SeqFeature::Store::new
> > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store.pm:358
> > STACK toplevel /usr/bin/bp_seqfeature_load.pl:62
> > -------------------------------------------
> > I can login into mysql, and manually run insert commands to add new
> entries
> > to the hg18 database, but the perl program doesn't seem to be able to
> change
> > the database anymore. bp_seqfeature_load.pl only worked once when I
> > initially first loaded the human genome, but doesn't work when I now try
> to
> > add the tracks and doesn't give me any diagnostic error messages.
> >
> >
> > -Sincerely,
> > Mao
> >
> >
> >
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