Hi, <br><br>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. <br>
<br>No matter how many times the <a href="http://bp_seqfeature.load.pl">bp_seqfeature.load.pl</a> program runs, the hg18 database refuses to change; all tables contain the exact same entries, and same number of entries as before.<br>
<br>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).<br><br>-Sincerely,<br>Mao<br><br><br><div class="gmail_quote">On Tue, Dec 16, 2008 at 4:03 PM, Dave Clements, GMOD Help Desk <span dir="ltr"><<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Mao,<br>
<br>
Can you send me a pointer to where you got your GFF3 files for the<br>
human genome, and a copy of the c_389.gff3 file?<br>
<br>
It certainly appears that bp_seqfeature_load.pl thinks it loaded 41<br>
features. Did the # of records in the feature table change at all as<br>
a result of the c_389.gff3 load?<br>
<br>
Thanks,<br>
<br>
Dave C.<br>
<br>
Was this helpful? Let us know at <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
<div><div></div><div class="Wj3C7c"><br>
<br>
<br>
On Thu, Dec 11, 2008 at 4:43 PM, Mao Mao <<a href="mailto:themao@gmail.com">themao@gmail.com</a>> wrote:<br>
> Hi,<br>
><br>
> I recently deleted and recreated a hg18 mysql database to hold my data.<br>
> After I successfully uploaded the hg18 genome, I can get the<br>
> bp_seqfeature_load.pl program to work anymore. I haven't changed the perl<br>
> program, and when I use it I get all normal messages and no error messages<br>
> such as below:<br>
> [gmao@pipeline Chimp HpaII]$ bp_seqfeature_load.pl -f -d hg18 c_389.gff3<br>
> loading c_389.gff3...<br>
> 41 features loaded in<br>
> 0.00s Building object<br>
> tree... 0.00s<br>
> Loading bulk data into database... 0.00s<br>
> load time: 0.07s<br>
><br>
> However, the hg18 mysql database isn't updated at all. I've looked through<br>
> all the tables (except feature and sequence) and nothing new was inserted.<br>
> The only thing in my database so far is the human genome, but none of the<br>
> tracks have managed to succesfully register into the database. I don't get<br>
> any typical error messages that might come from permission denied reasons:<br>
> [gmao@pipeline Chimp HpaII]$ bp_seqfeature_load.pl -f -d hg28 c_389.gff3<br>
> DBI connect('hg28','',...) failed: Access denied for user ''@'localhost' to<br>
> database 'hg28' at<br>
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/<a href="http://mysql.pm" target="_blank">mysql.pm</a> line 211<br>
><br>
> -------------------- EXCEPTION --------------------<br>
> MSG: Access denied for user ''@'localhost' to database 'hg28'<br>
> STACK Bio::DB::SeqFeature::Store::DBI::mysql::init<br>
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/DBI/<a href="http://mysql.pm:211" target="_blank">mysql.pm:211</a><br>
> STACK Bio::DB::SeqFeature::Store::new<br>
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store.pm:358<br>
> STACK toplevel /usr/bin/bp_seqfeature_load.pl:62<br>
> -------------------------------------------<br>
> I can login into mysql, and manually run insert commands to add new entries<br>
> to the hg18 database, but the perl program doesn't seem to be able to change<br>
> the database anymore. bp_seqfeature_load.pl only worked once when I<br>
> initially first loaded the human genome, but doesn't work when I now try to<br>
> add the tracks and doesn't give me any diagnostic error messages.<br>
><br>
><br>
> -Sincerely,<br>
> Mao<br>
><br>
><br>
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</blockquote></div><br>