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From: Vikas <vv...@cs...> - 2003-05-20 06:10:01
|
Hi, While reading through the Bio::Graphics HOWTO, I came across this line by Lincoln which refers to gbrowse for image maps. I checked the thing and was wondering about how to use it in my case. The scenario is that I have to generate clone and vector maps and have to display features and restriction enzymes and I want all of them to be clickable. Now, as from gbrose documentation, I can see that I can write a GFF format file for that but is it possible to generate images (with image maps) on the fly from dynamically generated GFF files? Thanks and would really appreciate your help. Regards, Vikas. |
From: David L. <dav...@ya...> - 2003-05-17 01:37:33
|
Hi Lincoln The problem (which isnt a problem) was I misplaced one of the modules from the GGB cvs in the wrong directories within the bioperl cvs download. thanks --- Lincoln Stein <ls...@cs...> wrote: > Hi David, > > What was the problem? I'd like to fix the install > instructions to avoid this > scenario from repeating itself. > > Lincoln > > On Tuesday 13 May 2003 11:19 pm, David Lyon wrote: > > I finally got it working... > > Thanks Lincoln and Scott for your help > > > > > > > > Lincoln Stein <ls...@cs...> wrote: > > Hi David, > > > > Let's focus on the main gbrowse script for the > moment. What queries make it > > stop? Does it stop with a crash, or just hang > trying to fetch data? > > > > I'm thinking that if you are trying to do a > keyword search, then there is a > > bug in some recent CVS versions of gbrowse that is > fixed by updating to the > > very latest CVS (as of this weekend). > > > > Lincoln > > > > On Tuesday 13 May 2003 03:48 pm, David Lyon wrote: > > > Hello > > > > > > I am trying to implement gbrowse and I am stuck. > I > > > have a few questions. > > > > > > I have populated a mysql with the sample data > provided > > > > > > > > > Running the script gbrowse_img > > > I get the correct image return with > > > gbrowse_img?source=yeast;name=II > > > returns the overview image as seen on wormbase. > > > > > > > > > I get an empty image with a scale and key BUT no > genes > > > > > > gbrowse_img?source=yeast;name=I > > > Why arent any of the features showing? > > > > > > Running gbrowse: > > > The web page loads OK but when I query the web > page, > > > it loads and then stops just a point just below > the > > > search button just at the point where the images > are > > > suppose to appear next. > > > > > > Anyone with ideas why no images are returned > with > > > gbrowse? > > > > > > > > > There are no indication of errors in web logs > > > Using debug =1 gives no clear indiction of an > error. > > > dumping fasta dna sequences work from gb_browse. > > > > > > Any suggestions would be appreciated > > > > > > Cheers > > > > > > __________________________________ > > > Do you Yahoo!? > > > The New Yahoo! Search - Faster. Easier. Bingo. > > > http://search.yahoo.com > > > > > > > > > > ------------------------------------------------------- > > > Enterprise Linux Forum Conference & Expo, June > 4-6, 2003, Santa Clara > > > The only event dedicated to issues related to > Linux enterprise solutions > > > www.enterpriselinuxforum.com > > > > > > _______________________________________________ > > > Gmod-gbrowse mailing list > > > Gmo...@li... > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- > ======================================================================== > Lincoln D. Stein Cold > Spring Harbor Laboratory > ls...@cs... Cold Spring > Harbor, NY > ======================================================================== > __________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. http://search.yahoo.com |
From: <ji...@dn...> - 2003-05-16 20:54:21
|
Dr. Stein, Yes, this time I got a lot of sequences within my error log. Based on the part what I looked through carefully, I briefly list the messages as below: $ref - gives the sequence names that I loaded into my database (like "I", "II", etc.) $off - gives numbers that from the first sequence's 0, then 2000, 4000, ... till the end, then does the same for next sequence ... till my last sequence. $d - gives pieces of 2000bp long sequences; the 1st piece matches 1-2000 of the sequence of "$ref" the 2nd piece matches 2001-4000 of the sequence of "$ref" ... $dna - the first piece of $ref is 2000bp long, and it is the same seq as $d from the second till the last piece, all is 2020bp long, with the last 2000bp exactly the same sequence as its $d (e.g. with the same $ref and $off, their $dna:21-2020bp is aligned with $d:1-2000bp ... The code of "warn "forward=@forward, reverse=@reverse\n";" after the "my @reverse = ..." line, shows that "@forward" and "@reverse" are empty. Here I copied pieces from my error log, for making my explanation clearer: ref=I, off=0, d=CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAAATCTTTAAATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAACCCGA...,dna=CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATCCCTAAA TCCCTAAATCTTTAAATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAACCCGAAACCGGTTTCTCTGGTTGAAAATCATTGTGTATATAATGATAATTTTATCGTTTTTATGTAATTGCTTATTGTTGTGTG... ref=I, off=2000, d=TGTTTCATGTGATATCAAACCAGCGACAACAAAAGTATTATTCCCCTCATTATGTTTGACTCCTATTATATTTTTATTTTAATTTTTTTCACTATCATCTTTCTTGCA...dna=ACCATGTATTCATAGTAAAATGTTTCATGTGATATCAAACCAGCGACAACAAAAGTATTATTCCCCTCATTATGTTTGACTCCTATTATATTTTTATTTTAATTTTTTTCACTATCATCTTTCTTGCAATGAAAGTCCCATATATTGGTCAACATTTCAAA... ... ref=II, off=0, d=..., dna=... ref=II, off=2000, d=..., dna=... ... For "warn "forward=@forward, reverse=@reverse\n";" the same message "forward=, reverse=" showed ten times. Jing ps: Glad to get chance to learn from you. :) > Hi Jing, > > We're getting there. Now place the following debugging code into the > auto_find() subroutine. Just before the line "my @forward = > $self->exact_matches)" put: > > warn "ref=$ref, off=$off, d=$d, dna=$dna\n"; > (this is going to generate a tremendous amount of debugging information). > > Then after the "my @reverse = ..." line, put > > warn "forward=@forward, reverse=@reverse\n"; > > Thanks, > > Lincoln |
From: sureshraja x. <sur...@ya...> - 2003-05-16 17:27:11
|
Hi Dr.Lincoln Stein, The following is the error message i got in the error log when i tried to access the human db for any of the chromosome data. ------------- EXCEPTION ------------- MSG: Unable to load transcript_density{bin:exon:NCBI} aggregator: syntax error at (eval 24) line 1, near "require Bio::DB::GFF::Aggregator::transcript_density{" STACK Bio::DB::GFF::add_aggregator /usr/lib/perl5/site_perl/5.6.1/Bio/DB/GFF.pm:1748 STACK Bio::DB::GFF::new /usr/lib/perl5/site_perl/5.6.1/Bio/DB/GFF.pm:563 STACK (eval) /var/www/cgi-bin/gbrowse:1264 STACK main::open_database /var/www/cgi-bin/gbrowse:1264 STACK main::get_settings /var/www/cgi-bin/gbrowse:413 STACK toplevel /var/www/cgi-bin/gbrowse:126 Thanks, Suresh --- Lincoln Stein <ls...@cs...> wrote: > Hi Sureshraja, > > Please send an excerpt from the web server error log > file showing what errors > are issued when you get the internal server error. > > Lincoln > > On Thursday 15 May 2003 12:06 am, sureshraja xavier > wrote: > > --0-1898640931-1052971583=:35847 > > Content-Type: text/plain; charset=us-ascii > > Content-Id: > > Content-Disposition: inline > > > > Hello, > > After i successfully installed gbrowse on my > > server. I tried to install the human database. I > ran > > the command process_ncbi_human.pl and the > > following happened: > > > > 1) The command gave error messages and the > human.gff > > file that was created contained erroneous data. > > (Note:I have put the error messages on the console > and > > contents of human.gff together in the file > attachment: > > console_output_and_human_gff) > > > > Since, the above approach gave errors, I > followed a > > different approach, which I am not sure whether it > is > > right. It is as follows: > > (Note: The contents of what I did is in the second > > attachment different_approach.) > > > > 1) I ran the fast_load_gff.pl command using the > > human.gff.tar.gz downloaded from the gmod website. > The > > number of rows inserted in each of the tables > after > > running the fast_load_gff.pl command is also > specified > > in the file. > > > > But when i accessed the human db from the > gbrowse, > > it gave the "Internal Server Error". As you said > the > > error_log contained a lot of messages, concerned > with > > this "Internal Server Error". I have also included > > that in the second attachment > > > > Thank you very much for your support. > > > > Cheers, > > Suresh > > > > > > __________________________________ > > Do you Yahoo!? > > The New Yahoo! Search - Faster. Easier. Bingo. > > http://search.yahoo.com > > --0-1898640931-1052971583=:35847 > > Content-Type: text/plain; > name="console_output_and_human_gff.txt" > > Content-Description: > console_output_and_human_gff.txt > > Content-Disposition: inline; > filename="console_output_and_human_gff.txt" > > > > PROCESS_NCBI_HUMAN.PL CONSOLE OUTPUT > > ------------------------------------ > > > > > > /../path/process_ncbi_human.pl --locuslink > LL.out.hs.gz chr*sequence.gz > > > human.gff > > > > 1000 total features parsed. Now doing chromosome 1 > > 3000 total features parsed. Now doing chromosome 1 > > 4000 total features parsed. Now doing chromosome 1 > > > > 1328000: Command not found. > > 1329000 total features parsed. > > Now doing chromosome 6 > > 1329000: Command not found. > > Can't call method "print" on an undefined value at > > > /opt/tars/Generic-Genome-Browser-1.50/blib/script/process_ncbi_human.pl > > line 313, <> line 46059649. > > > > > > HUMAN.GFF CONTENTS > > ------------------ > > Preparing input and output streams: > > @ > > @ //I added this statement: This symbol '@' occurs > for a few more lines // > > @ > > can't get chrom name from filename > > 'chrUn_sequence.gz', SKIPPING^M--100 LocusLink > records loaded^M--200 > > LocusLink records loaded^M--300 LocusLink records > loaded^M--400 LocusLink > > records loaded^M--500 LocusLink records > loaded^M--600 LocusLink records > > loaded^M--700 LocusLink records loaded^M--800 > LocusLink records > > loaded^M--900 LocusLink records loaded^M--1000 > LocusLink records > > loaded^M--1100 LocusLink records loaded^M--1200 > > -- > ======================================================================== > Lincoln D. Stein Cold > Spring Harbor Laboratory > ls...@cs... Cold Spring > Harbor, NY > ======================================================================== > ===== SURESH RAJA XAVIER 4302, COLLEGE MAIN APT #357, BRYAN, TEXAS - 77801 USA Resi: 1-979-268-2234 Office:1-979-458-1383 __________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. http://search.yahoo.com |
From: Lincoln S. <ls...@cs...> - 2003-05-16 13:06:53
|
Hi David, What was the problem? I'd like to fix the install instructions to avoid = this=20 scenario from repeating itself. Lincoln On Tuesday 13 May 2003 11:19 pm, David Lyon wrote: > I finally got it working... > Thanks Lincoln and Scott for your help > > > > Lincoln Stein <ls...@cs...> wrote: > Hi David, > > Let's focus on the main gbrowse script for the moment. What queries mak= e it > stop? Does it stop with a crash, or just hang trying to fetch data? > > I'm thinking that if you are trying to do a keyword search, then there = is a > bug in some recent CVS versions of gbrowse that is fixed by updating to= the > very latest CVS (as of this weekend). > > Lincoln > > On Tuesday 13 May 2003 03:48 pm, David Lyon wrote: > > Hello > > > > I am trying to implement gbrowse and I am stuck. I > > have a few questions. > > > > I have populated a mysql with the sample data provided > > > > > > Running the script gbrowse_img > > I get the correct image return with > > gbrowse_img?source=3Dyeast;name=3DII > > returns the overview image as seen on wormbase. > > > > > > I get an empty image with a scale and key BUT no genes > > > > gbrowse_img?source=3Dyeast;name=3DI > > Why arent any of the features showing? > > > > Running gbrowse: > > The web page loads OK but when I query the web page, > > it loads and then stops just a point just below the > > search button just at the point where the images are > > suppose to appear next. > > > > Anyone with ideas why no images are returned with > > gbrowse? > > > > > > There are no indication of errors in web logs > > Using debug =3D1 gives no clear indiction of an error. > > dumping fasta dna sequences work from gb_browse. > > > > Any suggestions would be appreciated > > > > Cheers > > > > __________________________________ > > Do you Yahoo!? > > The New Yahoo! Search - Faster. Easier. Bingo. > > http://search.yahoo.com > > > > > > ------------------------------------------------------- > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > > The only event dedicated to issues related to Linux enterprise soluti= ons > > www.enterpriselinuxforum.com > > > > _______________________________________________ > > Gmod-gbrowse mailing list > > Gmo...@li... > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
From: Lincoln S. <ls...@cs...> - 2003-05-16 13:06:12
|
Hi Jing, We're getting there. Now place the following debugging code into the=20 auto_find() subroutine. Just before the line "my @forward =3D=20 $self->exact_matches)" put: warn "ref=3D$ref, off=3D$off, d=3D$d, dna=3D$dna\n"; (this is going to generate a tremendous amount of debugging information). Then after the "my @reverse =3D ..." line, put warn "forward=3D@forward, reverse=3D@reverse\n"; Thanks, Lincoln On Thursday 15 May 2003 03:41 pm, ji...@dn... wrote: > Okay, here are what I got: > > 1) when after the call to valid_oligo() > =3D>auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 73= =2E > > 2) When after the call to $sth->execute() > =3D>auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 87 > > > 3) after the call to exact_matches() > When I tried this, Something shows different: > > - if I ONLY put the warning after "my @forward =3D $self->exact_matc= hes > ($dna,$oligo);" > * the message "auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line > 104." > * the same message will show _10 times_ > > - or, if ONLY put it after " my @reverse =3D $self->exact_matches > ($dna,$reversec);" > * the message "auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line > 106." > * It will show _10 times_ > > > - If I put the warning after both "my @forward =3D ..." AND "my @rev= erse > =3D ..." > the message will alternatively show as the above for "forward" and > "reverse", > as its total number of ten. E.g: I will get: > > auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104. > auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106. > auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104. > auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106. > auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104. > auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106. > auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104. > auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106. > auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104. > auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106. > > > Jing > > > > > > > > Lincoln Stein > <lstein@cshl.o To: ji...@dn... > rg> cc: =20 > gmo...@li... Subject: Re: [Gmod-gbrowse] > oligofinder problem 05/15/2003 > 01:46 PM > Please respond > to lstein > > > > > > > OK, could you now try putting the warning messages in other places insi= de > that > routine? Try putting it: > > 1) after the call to valid_oligo() > 2) after the call to $sth->execute() > 3) after the call to exact_matches() > > I'm trying to determine where the call is failing. One possible issue = is > the > way that the plugin tries to determine the chromosome-length sequences, > which > is the following crufty call: > > sub get_chroms { > my $self =3D shift; > my $db =3D shift; > my $dbi =3D $db->features_db; > > my $source =3D $self->browser_config()->source; > return @{$self->{chroms}{$source}} if ref($self->{chroms}{$source}); > my $chroms =3D $dbi->selectcol_arrayref('select fref from fdna group = by > fref > having count(fref)>10'); > $self->{chroms}{$source} =3D $chroms; > return @$chroms; > } > > This doesn't look very reliable to me. > > Thanks, > > Lincoln > > On Wednesday 14 May 2003 09:29 am, ji...@dn... wrote: > > I've tried, and here is the message what I got from server error.log: > > > > "auto_find() called with cctcgacttgaggttttccgc at > > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 71." > > > > I get the exactly same message when I search for oligo in both lower = and > > upper cases. > > > > From GBrowse, the whole message is: > > "The landmark named CCTCGACTTGAGGTTTTCCGC (via Short Oligos search) i= s > > not > > > recognized. See the help pages for suggestions" > > > > Jing > > > > > > > > > > Lincoln Stein > > <lstein@cshl.o To: jingyu@dnalandmarks.= ca, > > rg> > > gmo...@li... cc: > > 05/13/2003 Subject: Re: [Gmod-gbrow= se] > > oligofinder problem 06:09 PM > > Please respond > > to lstein > > > > > > > > > > > > > > Could you put a warning into the OligoFinder.pm auto_find() subroutin= e > > and > > > check whether the search routine is even being called? > > > > # auto_find() does the actual work > > # It is also called by the main page as a last resort when the user > > # types something into the search box that isn't recognized. > > sub auto_find { > > my $self =3D shift; > > my $oligo =3D lc shift; > > > > warn "auto_find() called with $oligo";^^^^^^^^^ > > > > $self->valid_oligo($oligo) or return; > > > > (my $reversec =3D $oligo) =3D~ tr/gatcGATC/ctagCTAG/; > > $reversec =3D reverse $reversec; > > my $length =3D length $oligo; > > ... > > > > You should see this message appear in the server error log. > > > > Lincoln > > > > On Monday 12 May 2003 05:23 am, ji...@dn... wrote: > > > > Do you have the OligoFinder plugin listed among the > > > > other plugins in your configuration file? > > > > > > Yes. I do. > > > > > > Jing > > > > > > > > > > > > > > > Lincoln Stein > > > <lstein@cshl.o To: > > ji...@dn..., > > > > rg> > > > gmo...@li... cc: > > > 05/11/2003 Subject: Re: > > [Gmod-gbrowse] > > > > oligofinder problem 08:39 PM > > > Please respond > > > to lstein > > > > > > > > > > > > > > > > > > > > > Here's a silly question. Do you have the OligoFinder plugin listed > > among > > > > the > > > other plugins in your configuration file? > > > > > > plugins =3D FastaDumper > > > OligoFinder RestrictionAnnotator > > > GFFDumper GeneFinder > > > BatchDumper > > > > > > > > > Lincoln > > > > > > On Wednesday 07 May 2003 03:14 pm, ji...@dn... wrote: > > > > Hello, > > > > > > > > I get the same problem about OligoFinder. I am using bioperl 1.2= and > > I > > > > do > > > > > > > load sequence in my database. I've tried on both 1.49 and 1.50, = with > > > > > > 21bp > > > > > > > oligo in both upper and lower cases. But I always get info as > > > > "landmark > > > > > > not recognized". > > > > > > > > Jing > > > > > > > > > > Also, the oligo-searching function doesn't work. It keeps com= ing > > up > > > > > > > "landmark not recognized". I vaguely remember it working in t= he > > > > 1.49 > > > > > > > > version of GBrowse. Now I'm using v1.50 and bioperl 1.2.1. > > > > > > > > ------------------------------------------------------- > > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa C= lara > > > > The only event dedicated to issues related to Linux enterprise > > > > solutions > > > > > > www.enterpriselinuxforum.com > > > > > > > > _______________________________________________ > > > > Gmod-gbrowse mailing list > > > > Gmo...@li... > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
From: David L. <dav...@ya...> - 2003-05-16 04:06:29
|
OK everything is fully functional now and its really great! I made a silly mistake, which I am too embarassed to admit. Thanks to you and the GMOD team for providing a first rate set of software! --- Lincoln Stein <ls...@cs...> wrote: > Hi David, > > This is very strange. The first thing to do is to > check that you've actually > updated bioperl as well as gbrowse. If you use the > CVS version of gbrowse, > then it depends on features that are being developed > in parallel in bioperl. > > The server error log may contain some messages that > indicate what's going > wrong. Could you have a look and see? > > Lincoln > > > On Wednesday 14 May 2003 09:36 pm, David Lyon wrote: > > Any help with the following would be > appreciated... > > > > I must of done something silly. I managed to get > the gbrowse working apart > > from the fact that I cant get the detailed view > image html links working. I > > have to comment out "do_map" in the subroutine sub > detail_panel in the > > gbrowse script because if I leave it in, the > detail image disappears. Now > > of course by commenting out do_map => 1 the > detailed image appears but > > doesnt have any html links. > > > > I had a look at Bio::Graphics::Browser and > Bio::FeatureFile and couldnt > > find wh ats up. > > Does anyone have any suggestions? > > > > I am using the most uptodate versions of all the > modules in cvs and mysql > > yeast db. Thanks > > > > > > --------------------------------- > > Do you Yahoo!? > > The New Yahoo! Search - Faster. Easier. Bingo. > > -- > ======================================================================== > Lincoln D. Stein Cold > Spring Harbor Laboratory > ls...@cs... Cold Spring > Harbor, NY > ======================================================================== > __________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. http://search.yahoo.com |
From: <ji...@dn...> - 2003-05-15 19:28:10
|
Okay, here are what I got: 1) when after the call to valid_oligo() =>auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 73. 2) When after the call to $sth->execute() =>auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 87 3) after the call to exact_matches() When I tried this, Something shows different: - if I ONLY put the warning after "my @forward = $self->exact_matches ($dna,$oligo);" * the message "auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104." * the same message will show _10 times_ - or, if ONLY put it after " my @reverse = $self->exact_matches ($dna,$reversec);" * the message "auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106." * It will show _10 times_ - If I put the warning after both "my @forward = ..." AND "my @reverse = ..." the message will alternatively show as the above for "forward" and "reverse", as its total number of ten. E.g: I will get: auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104. auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106. auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104. auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106. auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104. auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106. auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104. auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106. auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 104. auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 106. Jing Lincoln Stein <lstein@cshl.o To: ji...@dn... rg> cc: gmo...@li... Subject: Re: [Gmod-gbrowse] oligofinder problem 05/15/2003 01:46 PM Please respond to lstein OK, could you now try putting the warning messages in other places inside that routine? Try putting it: 1) after the call to valid_oligo() 2) after the call to $sth->execute() 3) after the call to exact_matches() I'm trying to determine where the call is failing. One possible issue is the way that the plugin tries to determine the chromosome-length sequences, which is the following crufty call: sub get_chroms { my $self = shift; my $db = shift; my $dbi = $db->features_db; my $source = $self->browser_config()->source; return @{$self->{chroms}{$source}} if ref($self->{chroms}{$source}); my $chroms = $dbi->selectcol_arrayref('select fref from fdna group by fref having count(fref)>10'); $self->{chroms}{$source} = $chroms; return @$chroms; } This doesn't look very reliable to me. Thanks, Lincoln On Wednesday 14 May 2003 09:29 am, ji...@dn... wrote: > I've tried, and here is the message what I got from server error.log: > > "auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 71." > > I get the exactly same message when I search for oligo in both lower and > upper cases. > > From GBrowse, the whole message is: > "The landmark named CCTCGACTTGAGGTTTTCCGC (via Short Oligos search) is not > recognized. See the help pages for suggestions" > > Jing > > > > > Lincoln Stein > <lstein@cshl.o To: ji...@dn..., > rg> > gmo...@li... cc: > 05/13/2003 Subject: Re: [Gmod-gbrowse] > oligofinder problem 06:09 PM > Please respond > to lstein > > > > > > > Could you put a warning into the OligoFinder.pm auto_find() subroutine and > check whether the search routine is even being called? > > # auto_find() does the actual work > # It is also called by the main page as a last resort when the user > # types something into the search box that isn't recognized. > sub auto_find { > my $self = shift; > my $oligo = lc shift; > > warn "auto_find() called with $oligo";^^^^^^^^^ > > $self->valid_oligo($oligo) or return; > > (my $reversec = $oligo) =~ tr/gatcGATC/ctagCTAG/; > $reversec = reverse $reversec; > my $length = length $oligo; > ... > > You should see this message appear in the server error log. > > Lincoln > > On Monday 12 May 2003 05:23 am, ji...@dn... wrote: > > > Do you have the OligoFinder plugin listed among the > > > other plugins in your configuration file? > > > > Yes. I do. > > > > Jing > > > > > > > > > > Lincoln Stein > > <lstein@cshl.o To: ji...@dn..., > > rg> > > gmo...@li... cc: > > 05/11/2003 Subject: Re: [Gmod-gbrowse] > > oligofinder problem 08:39 PM > > Please respond > > to lstein > > > > > > > > > > > > > > Here's a silly question. Do you have the OligoFinder plugin listed among > > the > > other plugins in your configuration file? > > > > plugins = FastaDumper > > OligoFinder RestrictionAnnotator > > GFFDumper GeneFinder > > BatchDumper > > > > > > Lincoln > > > > On Wednesday 07 May 2003 03:14 pm, ji...@dn... wrote: > > > Hello, > > > > > > I get the same problem about OligoFinder. I am using bioperl 1.2 and I > > > > do > > > > > load sequence in my database. I've tried on both 1.49 and 1.50, with > > > > 21bp > > > > > oligo in both upper and lower cases. But I always get info as > > "landmark > > > > not recognized". > > > > > > Jing > > > > > > > > Also, the oligo-searching function doesn't work. It keeps coming up > > > > > "landmark not recognized". I vaguely remember it working in the > > 1.49 > > > > > > version of GBrowse. Now I'm using v1.50 and bioperl 1.2.1. > > > > > > ------------------------------------------------------- > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > > > The only event dedicated to issues related to Linux enterprise > > solutions > > > > www.enterpriselinuxforum.com > > > > > > _______________________________________________ > > > Gmod-gbrowse mailing list > > > Gmo...@li... > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- ======================================================================== Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs... Cold Spring Harbor, NY ======================================================================== |
From: Lincoln S. <ls...@cs...> - 2003-05-15 17:59:54
|
OK, could you now try putting the warning messages in other places inside= that=20 routine? Try putting it: =091) after the call to valid_oligo() =092) after the call to $sth->execute() =093) after the call to exact_matches() I'm trying to determine where the call is failing. One possible issue is= the=20 way that the plugin tries to determine the chromosome-length sequences, w= hich=20 is the following crufty call: sub get_chroms { my $self =3D shift; my $db =3D shift; my $dbi =3D $db->features_db; my $source =3D $self->browser_config()->source; return @{$self->{chroms}{$source}} if ref($self->{chroms}{$source}); my $chroms =3D $dbi->selectcol_arrayref('select fref from fdna group by= fref=20 having count(fref)>10'); $self->{chroms}{$source} =3D $chroms; return @$chroms; } This doesn't look very reliable to me. Thanks, Lincoln On Wednesday 14 May 2003 09:29 am, ji...@dn... wrote: > I've tried, and here is the message what I got from server error.log: > > "auto_find() called with cctcgacttgaggttttccgc at > /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 71." > > I get the exactly same message when I search for oligo in both lower an= d > upper cases. > > From GBrowse, the whole message is: > "The landmark named CCTCGACTTGAGGTTTTCCGC (via Short Oligos search) is = not > recognized. See the help pages for suggestions" > > Jing > > > > > Lincoln Stein > <lstein@cshl.o To: ji...@dn...= , > rg> =20 > gmo...@li... cc: > 05/13/2003 Subject: Re: [Gmod-gbrowse= ] > oligofinder problem 06:09 PM > Please respond > to lstein > > > > > > > Could you put a warning into the OligoFinder.pm auto_find() subroutine = and > check whether the search routine is even being called? > > # auto_find() does the actual work > # It is also called by the main page as a last resort when the user > # types something into the search box that isn't recognized. > sub auto_find { > my $self =3D shift; > my $oligo =3D lc shift; > > warn "auto_find() called with $oligo";^^^^^^^^^ > > $self->valid_oligo($oligo) or return; > > (my $reversec =3D $oligo) =3D~ tr/gatcGATC/ctagCTAG/; > $reversec =3D reverse $reversec; > my $length =3D length $oligo; > ... > > You should see this message appear in the server error log. > > Lincoln > > On Monday 12 May 2003 05:23 am, ji...@dn... wrote: > > > Do you have the OligoFinder plugin listed among the > > > other plugins in your configuration file? > > > > Yes. I do. > > > > Jing > > > > > > > > > > Lincoln Stein > > <lstein@cshl.o To: jingyu@dnalandmarks.= ca, > > rg> > > gmo...@li... cc: > > 05/11/2003 Subject: Re: [Gmod-gbrow= se] > > oligofinder problem 08:39 PM > > Please respond > > to lstein > > > > > > > > > > > > > > Here's a silly question. Do you have the OligoFinder plugin listed a= mong > > the > > other plugins in your configuration file? > > > > plugins =3D FastaDumper > > OligoFinder RestrictionAnnotator > > GFFDumper GeneFinder > > BatchDumper > > > > > > Lincoln > > > > On Wednesday 07 May 2003 03:14 pm, ji...@dn... wrote: > > > Hello, > > > > > > I get the same problem about OligoFinder. I am using bioperl 1.2 a= nd I > > > > do > > > > > load sequence in my database. I've tried on both 1.49 and 1.50, wi= th > > > > 21bp > > > > > oligo in both upper and lower cases. But I always get info as > > "landmark > > > > not recognized". > > > > > > Jing > > > > > > > > Also, the oligo-searching function doesn't work. It keeps comin= g up > > > > > "landmark not recognized". I vaguely remember it working in the > > 1.49 > > > > > > version of GBrowse. Now I'm using v1.50 and bioperl 1.2.1. > > > > > > ------------------------------------------------------- > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Cla= ra > > > The only event dedicated to issues related to Linux enterprise > > solutions > > > > www.enterpriselinuxforum.com > > > > > > _______________________________________________ > > > Gmod-gbrowse mailing list > > > Gmo...@li... > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
From: Gudmundur A. T. <mu...@cs...> - 2003-05-15 17:38:45
|
Lincoln. I do not have a version of the script that works on the current NCBI-annotation, no. However, I was just looking at the NCBI annotation FTP-downloads for build33, in preparation for revising that script so that I can update GBrowse on snp.cshl.org to build33. NCBI has indeed changed their format drastically, that is correct. They now have a couple of dozen files available, each containing data for a single feature type. These replace the all-features-on-chromosome files that they used to have. It will be some work adapting the script (possibly rewriting it entirely) to handle this new format/layout, but I will tackle that task over the weekend or next week. Will report on gmod-devel/gmod-gbrowse once I am done. Mummi, CSHL On Thursday, May 15, 2003, at 13:01 America/New_York, Lincoln Stein wrote: > Hi Mummi, > > It looks like process_ncbi_human.pl needs to be updated or removed. > Is there > a newer version of this script available? > > Lincoln > > On Thursday 15 May 2003 09:40 am, Scott Cain wrote: >> Suresh, >> >> I have bad news for you on both approaches you used. I believe the >> process_human_ncbi.pl script is out of date, as ncbi changed their >> file >> format since that was written. I believe one of us is working on a >> new >> version. >> >> As for your second approach, there are two problems even before you >> get >> to the aggregator problem mentioned in the error_log. First, the >> human >> data is quite out of date, and I have noticed small formatting >> problems >> with the gff files. If you are using MySQL as a backend, you probably >> won't notice them though (MySQL ignores them). One more problem that >> I >> just noticed is that you are loading fasta files with the human gff. >> Since there is not a copy of the human fastas on the gmod website, I >> would have to assume that the DNA sequence and the gff annotations are >> out of sync. >> >> As for exactly why the transcript_density aggregator failed, I am not >> sure, though it certainly may have to do with the problems I mentioned >> above. Perhaps Lincoln could shed more light on this. >> >> Scott >> >> On Thu, 2003-05-15 at 00:06, sureshraja xavier wrote: >>> Hello, >>> After i successfully installed gbrowse on my >>> server. I tried to install the human database. I ran >>> the command process_ncbi_human.pl and the >>> following happened: >>> >>> 1) The command gave error messages and the human.gff >>> file that was created contained erroneous data. >>> (Note:I have put the error messages on the console and >>> contents of human.gff together in the file attachment: >>> console_output_and_human_gff) >>> >>> Since, the above approach gave errors, I followed a >>> different approach, which I am not sure whether it is >>> right. It is as follows: >>> (Note: The contents of what I did is in the second >>> attachment different_approach.) >>> >>> 1) I ran the fast_load_gff.pl command using the >>> human.gff.tar.gz downloaded from the gmod website. The >>> number of rows inserted in each of the tables after >>> running the fast_load_gff.pl command is also specified >>> in the file. >>> >>> But when i accessed the human db from the gbrowse, >>> it gave the "Internal Server Error". As you said the >>> error_log contained a lot of messages, concerned with >>> this "Internal Server Error". I have also included >>> that in the second attachment >>> >>> Thank you very much for your support. >>> >>> Cheers, >>> Suresh >>> >>> >>> __________________________________ >>> Do you Yahoo!? >>> The New Yahoo! Search - Faster. Easier. Bingo. >>> http://search.yahoo.com >>> >>> _____________________________________________________________________ >>> _ >>> >>> PROCESS_NCBI_HUMAN.PL CONSOLE OUTPUT >>> ------------------------------------ >>> >>> >>> /../path/process_ncbi_human.pl --locuslink LL.out.hs.gz >>> chr*sequence.gz > >>> human.gff >>> >>> 1000 total features parsed. Now doing chromosome 1 >>> 3000 total features parsed. Now doing chromosome 1 >>> 4000 total features parsed. Now doing chromosome 1 >>> >>> 1328000: Command not found. >>> 1329000 total features parsed. >>> Now doing chromosome 6 >>> 1329000: Command not found. >>> Can't call method "print" on an undefined value at >>> /opt/tars/Generic-Genome-Browser-1.50/blib/script/ >>> process_ncbi_human.pl >>> line 313, <> line 46059649. >>> >>> >>> HUMAN.GFF CONTENTS >>> ------------------ >>> Preparing input and output streams: >>> @ >>> @ //I added this statement: This symbol '@' occurs for a few more >>> lines >>> // @ >>> can't get chrom name from filename >>> 'chrUn_sequence.gz', SKIPPING^M--100 LocusLink records loaded^M--200 >>> LocusLink records loaded^M--300 LocusLink records loaded^M--400 >>> LocusLink >>> records loaded^M--500 LocusLink records loaded^M--600 LocusLink >>> records >>> loaded^M--700 LocusLink records loaded^M--800 LocusLink records >>> loaded^M--900 LocusLink records loaded^M--1000 LocusLink records >>> loaded^M--1100 LocusLink records loaded^M--1200 . >>> . >>> . //I added this statement: data similar to the previous line >>> SKIPPING^M--100 LocusLink records loaded^M--200 LocusLink records >>> loaded^M--300 continues in a single line// . >>> Starting main loop: >>> >>> _____________________________________________________________________ >>> _ >>> >>> FAST_LOAD_GFF.PL CONSOLE OUTPUT >>> ------------------------------- >>> >>> ../PerlModules/bioperl-1.2/scripts/Bio-DB-GFF/fast_load_gff.pl -d >>> human >>> -f human_fasta human.gff.tar.gz >>> loading normalized group, type and attribute >>> information...ok >>> creating load file /usr/tmp/fdata.3854...ok >>> pausing for 0.5 sec...ok >>> opening load file for writing...ok >>> creating load file /usr/tmp/ftype.3854...ok >>> pausing for 0.5 sec...ok >>> opening load file for writing...ok >>> creating load file /usr/tmp/fgroup.3854...ok >>> pausing for 0.5 sec...ok >>> opening load file for writing...ok >>> creating load file /usr/tmp/fdna.3854...ok >>> pausing for 0.5 sec...ok >>> opening load file for writing...ok >>> creating load file /usr/tmp/fattribute.3854...ok >>> pausing for 0.5 sec...ok >>> opening load file for writing...ok >>> creating load file >>> /usr/tmp/fattribute_to_feature.3854...ok >>> pausing for 0.5 sec...ok >>> opening load file for writing...ok >>> Fast loading enabled >>> Loading fasta directory human_fasta >>> Warning: unable to close filehandle ARGV properly. >>> ERROR 1030 at line 1: Got error 139 from table handler >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> Warning: unable to close filehandle ARGV properly. >>> human_fasta: 24 records loaded >>> >>> >>> COUNT OF ROWS IN TABLES OF HUMAN DATABASE >>> ------------------------------------------ >>> fattribute = 2 >>> fattribute_to_feature = 2848127 >>> fdata = 3043825 >>> fdna = 0 >>> fgroup = 2341498 >>> fmeta = 0 >>> >>> >>> EXCEPTION IN WEB SERVER ERROR LOG >>> --------------------------------- >>> >>> ------------- EXCEPTION ------------- >>> MSG: Unable to load transcript_density{bin:exon:NCBI} aggregator: >>> syntax error a >>> t (eval 24) line 1, near "require >>> Bio::DB::GFF::Aggregator::transcript_density{" >>> >>> STACK Bio::DB::GFF::add_aggregator >>> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/GFF.pm: >>> 1748 >>> STACK Bio::DB::GFF::new >>> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/GFF.pm:563 >>> STACK (eval) /var/www/cgi-bin/gbrowse:1264 >>> STACK main::open_database /var/www/cgi-bin/gbrowse:1264 >>> STACK main::get_settings /var/www/cgi-bin/gbrowse:413 >>> STACK toplevel /var/www/cgi-bin/gbrowse:126 > > -- > ======================================================================= > = > Lincoln D. Stein Cold Spring Harbor > Laboratory > ls...@cs... Cold Spring Harbor, NY > ======================================================================= > = > > |
From: Lincoln S. <ls...@cs...> - 2003-05-15 17:14:33
|
Hi David, This is very strange. The first thing to do is to check that you've actu= ally=20 updated bioperl as well as gbrowse. If you use the CVS version of gbrows= e,=20 then it depends on features that are being developed in parallel in biope= rl. The server error log may contain some messages that indicate what's going= =20 wrong. Could you have a look and see? Lincoln On Wednesday 14 May 2003 09:36 pm, David Lyon wrote: > Any help with the following would be appreciated... > > I must of done something silly. I managed to get the gbrowse working ap= art > from the fact that I cant get the detailed view image html links workin= g. I > have to comment out "do_map" in the subroutine sub detail_panel in the > gbrowse script because if I leave it in, the detail image disappears. N= ow > of course by commenting out do_map =3D> 1 the detailed image appears bu= t > doesnt have any html links. > > I had a look at Bio::Graphics::Browser and Bio::FeatureFile and couldnt > find wh ats up. > Does anyone have any suggestions? > > I am using the most uptodate versions of all the modules in cvs and mys= ql > yeast db. Thanks > > > --------------------------------- > Do you Yahoo!? > The New Yahoo! Search - Faster. Easier. Bingo. --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
From: Lincoln S. <ls...@cs...> - 2003-05-15 17:09:07
|
Hi Sureshraja, Please send an excerpt from the web server error log file showing what er= rors=20 are issued when you get the internal server error. Lincoln On Thursday 15 May 2003 12:06 am, sureshraja xavier wrote: > --0-1898640931-1052971583=3D:35847 > Content-Type: text/plain; charset=3Dus-ascii > Content-Id: > Content-Disposition: inline > > Hello, > After i successfully installed gbrowse on my > server. I tried to install the human database. I ran > the command process_ncbi_human.pl and the > following happened: > > 1) The command gave error messages and the human.gff > file that was created contained erroneous data. > (Note:I have put the error messages on the console and > contents of human.gff together in the file attachment: > console_output_and_human_gff) > > Since, the above approach gave errors, I followed a > different approach, which I am not sure whether it is > right. It is as follows: > (Note: The contents of what I did is in the second > attachment different_approach.) > > 1) I ran the fast_load_gff.pl command using the > human.gff.tar.gz downloaded from the gmod website. The > number of rows inserted in each of the tables after > running the fast_load_gff.pl command is also specified > in the file. > > But when i accessed the human db from the gbrowse, > it gave the "Internal Server Error". As you said the > error_log contained a lot of messages, concerned with > this "Internal Server Error". I have also included > that in the second attachment > > Thank you very much for your support. > > Cheers, > Suresh > > > __________________________________ > Do you Yahoo!? > The New Yahoo! Search - Faster. Easier. Bingo. > http://search.yahoo.com > --0-1898640931-1052971583=3D:35847 > Content-Type: text/plain; name=3D"console_output_and_human_gff.txt" > Content-Description: console_output_and_human_gff.txt > Content-Disposition: inline; filename=3D"console_output_and_human_gff.t= xt" > > PROCESS_NCBI_HUMAN.PL CONSOLE OUTPUT > ------------------------------------ > > > /../path/process_ncbi_human.pl --locuslink LL.out.hs.gz chr*sequence.gz= > > human.gff > > 1000 total features parsed. Now doing chromosome 1 > 3000 total features parsed. Now doing chromosome 1 > 4000 total features parsed. Now doing chromosome 1 > > 1328000: Command not found. > 1329000 total features parsed. > Now doing chromosome 6 > 1329000: Command not found. > Can't call method "print" on an undefined value at > /opt/tars/Generic-Genome-Browser-1.50/blib/script/process_ncbi_human.pl > line 313, <> line 46059649. > > > HUMAN.GFF CONTENTS > ------------------ > Preparing input and output streams: > @ > @ //I added this statement: This symbol '@' occurs for a few more lines= // > @ > can't get chrom name from filename > 'chrUn_sequence.gz', SKIPPING^M--100 LocusLink records loaded^M--200 > LocusLink records loaded^M--300 LocusLink records loaded^M--400 LocusLi= nk > records loaded^M--500 LocusLink records loaded^M--600 LocusLink records > loaded^M--700 LocusLink records loaded^M--800 LocusLink records > loaded^M--900 LocusLink records loaded^M--1000 LocusLink records > loaded^M--1100 LocusLink records loaded^M--1200 --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
From: Lincoln S. <ls...@cs...> - 2003-05-15 17:06:02
|
Hi Mummi, It looks like process_ncbi_human.pl needs to be updated or removed. Is t= here=20 a newer version of this script available? Lincoln On Thursday 15 May 2003 09:40 am, Scott Cain wrote: > Suresh, > > I have bad news for you on both approaches you used. I believe the > process_human_ncbi.pl script is out of date, as ncbi changed their file > format since that was written. I believe one of us is working on a new > version. > > As for your second approach, there are two problems even before you get > to the aggregator problem mentioned in the error_log. First, the human > data is quite out of date, and I have noticed small formatting problems > with the gff files. If you are using MySQL as a backend, you probably > won't notice them though (MySQL ignores them). One more problem that I > just noticed is that you are loading fasta files with the human gff. > Since there is not a copy of the human fastas on the gmod website, I > would have to assume that the DNA sequence and the gff annotations are > out of sync. > > As for exactly why the transcript_density aggregator failed, I am not > sure, though it certainly may have to do with the problems I mentioned > above. Perhaps Lincoln could shed more light on this. > > Scott > > On Thu, 2003-05-15 at 00:06, sureshraja xavier wrote: > > Hello, > > After i successfully installed gbrowse on my > > server. I tried to install the human database. I ran > > the command process_ncbi_human.pl and the > > following happened: > > > > 1) The command gave error messages and the human.gff > > file that was created contained erroneous data. > > (Note:I have put the error messages on the console and > > contents of human.gff together in the file attachment: > > console_output_and_human_gff) > > > > Since, the above approach gave errors, I followed a > > different approach, which I am not sure whether it is > > right. It is as follows: > > (Note: The contents of what I did is in the second > > attachment different_approach.) > > > > 1) I ran the fast_load_gff.pl command using the > > human.gff.tar.gz downloaded from the gmod website. The > > number of rows inserted in each of the tables after > > running the fast_load_gff.pl command is also specified > > in the file. > > > > But when i accessed the human db from the gbrowse, > > it gave the "Internal Server Error". As you said the > > error_log contained a lot of messages, concerned with > > this "Internal Server Error". I have also included > > that in the second attachment > > > > Thank you very much for your support. > > > > Cheers, > > Suresh > > > > > > __________________________________ > > Do you Yahoo!? > > The New Yahoo! Search - Faster. Easier. Bingo. > > http://search.yahoo.com > > > > _____________________________________________________________________= _ > > > > PROCESS_NCBI_HUMAN.PL CONSOLE OUTPUT > > ------------------------------------ > > > > > > /../path/process_ncbi_human.pl --locuslink LL.out.hs.gz chr*sequence.= gz > > > human.gff > > > > 1000 total features parsed. Now doing chromosome 1 > > 3000 total features parsed. Now doing chromosome 1 > > 4000 total features parsed. Now doing chromosome 1 > > > > 1328000: Command not found. > > 1329000 total features parsed. > > Now doing chromosome 6 > > 1329000: Command not found. > > Can't call method "print" on an undefined value at > > /opt/tars/Generic-Genome-Browser-1.50/blib/script/process_ncbi_human.= pl > > line 313, <> line 46059649. > > > > > > HUMAN.GFF CONTENTS > > ------------------ > > Preparing input and output streams: > > @ > > @ //I added this statement: This symbol '@' occurs for a few more lin= es > > // @ > > can't get chrom name from filename > > 'chrUn_sequence.gz', SKIPPING^M--100 LocusLink records loaded^M--200 > > LocusLink records loaded^M--300 LocusLink records loaded^M--400 Locus= Link > > records loaded^M--500 LocusLink records loaded^M--600 LocusLink recor= ds > > loaded^M--700 LocusLink records loaded^M--800 LocusLink records > > loaded^M--900 LocusLink records loaded^M--1000 LocusLink records > > loaded^M--1100 LocusLink records loaded^M--1200 . > > . > > . //I added this statement: data similar to the previous line=20 > > SKIPPING^M--100 LocusLink records loaded^M--200 LocusLink records > > loaded^M--300 continues in a single line// . > > Starting main loop: > > > > _____________________________________________________________________= _ > > > > FAST_LOAD_GFF.PL CONSOLE OUTPUT > > ------------------------------- > > > > ../PerlModules/bioperl-1.2/scripts/Bio-DB-GFF/fast_load_gff.pl -d hum= an > > -f human_fasta human.gff.tar.gz > > loading normalized group, type and attribute > > information...ok > > creating load file /usr/tmp/fdata.3854...ok > > pausing for 0.5 sec...ok > > opening load file for writing...ok > > creating load file /usr/tmp/ftype.3854...ok > > pausing for 0.5 sec...ok > > opening load file for writing...ok > > creating load file /usr/tmp/fgroup.3854...ok > > pausing for 0.5 sec...ok > > opening load file for writing...ok > > creating load file /usr/tmp/fdna.3854...ok > > pausing for 0.5 sec...ok > > opening load file for writing...ok > > creating load file /usr/tmp/fattribute.3854...ok > > pausing for 0.5 sec...ok > > opening load file for writing...ok > > creating load file > > /usr/tmp/fattribute_to_feature.3854...ok > > pausing for 0.5 sec...ok > > opening load file for writing...ok > > Fast loading enabled > > Loading fasta directory human_fasta > > Warning: unable to close filehandle ARGV properly. > > ERROR 1030 at line 1: Got error 139 from table handler > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > Warning: unable to close filehandle ARGV properly. > > human_fasta: 24 records loaded > > > > > > COUNT OF ROWS IN TABLES OF HUMAN DATABASE > > ------------------------------------------ > > fattribute =3D 2 > > fattribute_to_feature =3D 2848127 > > fdata =3D 3043825 > > fdna =3D 0 > > fgroup =3D 2341498 > > fmeta =3D 0 > > > > > > EXCEPTION IN WEB SERVER ERROR LOG > > --------------------------------- > > > > ------------- EXCEPTION ------------- > > MSG: Unable to load transcript_density{bin:exon:NCBI} aggregator: > > syntax error a > > t (eval 24) line 1, near "require > > Bio::DB::GFF::Aggregator::transcript_density{" > > > > STACK Bio::DB::GFF::add_aggregator > > /usr/lib/perl5/site_perl/5.6.1/Bio/DB/GFF.pm: > > 1748 > > STACK Bio::DB::GFF::new > > /usr/lib/perl5/site_perl/5.6.1/Bio/DB/GFF.pm:563 > > STACK (eval) /var/www/cgi-bin/gbrowse:1264 > > STACK main::open_database /var/www/cgi-bin/gbrowse:1264 > > STACK main::get_settings /var/www/cgi-bin/gbrowse:413 > > STACK toplevel /var/www/cgi-bin/gbrowse:126 --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
From: Scott C. <ca...@cs...> - 2003-05-15 13:40:20
|
Suresh, I have bad news for you on both approaches you used. I believe the process_human_ncbi.pl script is out of date, as ncbi changed their file format since that was written. I believe one of us is working on a new version. As for your second approach, there are two problems even before you get to the aggregator problem mentioned in the error_log. First, the human data is quite out of date, and I have noticed small formatting problems with the gff files. If you are using MySQL as a backend, you probably won't notice them though (MySQL ignores them). One more problem that I just noticed is that you are loading fasta files with the human gff. Since there is not a copy of the human fastas on the gmod website, I would have to assume that the DNA sequence and the gff annotations are out of sync. As for exactly why the transcript_density aggregator failed, I am not sure, though it certainly may have to do with the problems I mentioned above. Perhaps Lincoln could shed more light on this. Scott On Thu, 2003-05-15 at 00:06, sureshraja xavier wrote: > Hello, > After i successfully installed gbrowse on my > server. I tried to install the human database. I ran > the command process_ncbi_human.pl and the > following happened: > > 1) The command gave error messages and the human.gff > file that was created contained erroneous data. > (Note:I have put the error messages on the console and > contents of human.gff together in the file attachment: > console_output_and_human_gff) > > Since, the above approach gave errors, I followed a > different approach, which I am not sure whether it is > right. It is as follows: > (Note: The contents of what I did is in the second > attachment different_approach.) > > 1) I ran the fast_load_gff.pl command using the > human.gff.tar.gz downloaded from the gmod website. The > number of rows inserted in each of the tables after > running the fast_load_gff.pl command is also specified > in the file. > > But when i accessed the human db from the gbrowse, > it gave the "Internal Server Error". As you said the > error_log contained a lot of messages, concerned with > this "Internal Server Error". I have also included > that in the second attachment > > Thank you very much for your support. > > Cheers, > Suresh > > > __________________________________ > Do you Yahoo!? > The New Yahoo! Search - Faster. Easier. Bingo. > http://search.yahoo.com > > ______________________________________________________________________ > > PROCESS_NCBI_HUMAN.PL CONSOLE OUTPUT > ------------------------------------ > > > /../path/process_ncbi_human.pl --locuslink LL.out.hs.gz chr*sequence.gz > human.gff > > 1000 total features parsed. Now doing chromosome 1 > 3000 total features parsed. Now doing chromosome 1 > 4000 total features parsed. Now doing chromosome 1 > > 1328000: Command not found. > 1329000 total features parsed. > Now doing chromosome 6 > 1329000: Command not found. > Can't call method "print" on an undefined value at > /opt/tars/Generic-Genome-Browser-1.50/blib/script/process_ncbi_human.pl line 313, <> line 46059649. > > > HUMAN.GFF CONTENTS > ------------------ > Preparing input and output streams: > @ > @ //I added this statement: This symbol '@' occurs for a few more lines // > @ > can't get chrom name from filename > 'chrUn_sequence.gz', SKIPPING^M--100 LocusLink records loaded^M--200 LocusLink records loaded^M--300 LocusLink records loaded^M--400 LocusLink records loaded^M--500 LocusLink records loaded^M--600 LocusLink records loaded^M--700 LocusLink records loaded^M--800 LocusLink records loaded^M--900 LocusLink records loaded^M--1000 LocusLink records loaded^M--1100 LocusLink records loaded^M--1200 > . > . > . //I added this statement: data similar to the previous line SKIPPING^M--100 LocusLink records loaded^M--200 LocusLink records loaded^M--300 continues in a single line// > . > Starting main loop: > > ______________________________________________________________________ > > FAST_LOAD_GFF.PL CONSOLE OUTPUT > ------------------------------- > > ../PerlModules/bioperl-1.2/scripts/Bio-DB-GFF/fast_load_gff.pl -d human > -f human_fasta human.gff.tar.gz > loading normalized group, type and attribute > information...ok > creating load file /usr/tmp/fdata.3854...ok > pausing for 0.5 sec...ok > opening load file for writing...ok > creating load file /usr/tmp/ftype.3854...ok > pausing for 0.5 sec...ok > opening load file for writing...ok > creating load file /usr/tmp/fgroup.3854...ok > pausing for 0.5 sec...ok > opening load file for writing...ok > creating load file /usr/tmp/fdna.3854...ok > pausing for 0.5 sec...ok > opening load file for writing...ok > creating load file /usr/tmp/fattribute.3854...ok > pausing for 0.5 sec...ok > opening load file for writing...ok > creating load file > /usr/tmp/fattribute_to_feature.3854...ok > pausing for 0.5 sec...ok > opening load file for writing...ok > Fast loading enabled > Loading fasta directory human_fasta > Warning: unable to close filehandle ARGV properly. > ERROR 1030 at line 1: Got error 139 from table handler > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > Warning: unable to close filehandle ARGV properly. > human_fasta: 24 records loaded > > > COUNT OF ROWS IN TABLES OF HUMAN DATABASE > ------------------------------------------ > fattribute = 2 > fattribute_to_feature = 2848127 > fdata = 3043825 > fdna = 0 > fgroup = 2341498 > fmeta = 0 > > > EXCEPTION IN WEB SERVER ERROR LOG > --------------------------------- > > ------------- EXCEPTION ------------- > MSG: Unable to load transcript_density{bin:exon:NCBI} aggregator: > syntax error a > t (eval 24) line 1, near "require > Bio::DB::GFF::Aggregator::transcript_density{" > > STACK Bio::DB::GFF::add_aggregator > /usr/lib/perl5/site_perl/5.6.1/Bio/DB/GFF.pm: > 1748 > STACK Bio::DB::GFF::new > /usr/lib/perl5/site_perl/5.6.1/Bio/DB/GFF.pm:563 > STACK (eval) /var/www/cgi-bin/gbrowse:1264 > STACK main::open_database /var/www/cgi-bin/gbrowse:1264 > STACK main::get_settings /var/www/cgi-bin/gbrowse:413 > STACK toplevel /var/www/cgi-bin/gbrowse:126 -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
From: sureshraja x. <sur...@ya...> - 2003-05-15 04:06:45
|
Hello, After i successfully installed gbrowse on my server. I tried to install the human database. I ran the command process_ncbi_human.pl and the following happened: 1) The command gave error messages and the human.gff file that was created contained erroneous data. (Note:I have put the error messages on the console and contents of human.gff together in the file attachment: console_output_and_human_gff) Since, the above approach gave errors, I followed a different approach, which I am not sure whether it is right. It is as follows: (Note: The contents of what I did is in the second attachment different_approach.) 1) I ran the fast_load_gff.pl command using the human.gff.tar.gz downloaded from the gmod website. The number of rows inserted in each of the tables after running the fast_load_gff.pl command is also specified in the file. But when i accessed the human db from the gbrowse, it gave the "Internal Server Error". As you said the error_log contained a lot of messages, concerned with this "Internal Server Error". I have also included that in the second attachment Thank you very much for your support. Cheers, Suresh __________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. http://search.yahoo.com |
From: David L. <dav...@ya...> - 2003-05-15 01:36:25
|
Any help with the following would be appreciated... I must of done something silly. I managed to get the gbrowse working apart from the fact that I cant get the detailed view image html links working. I have to comment out "do_map" in the subroutine sub detail_panel in the gbrowse script because if I leave it in, the detail image disappears. Now of course by commenting out do_map => 1 the detailed image appears but doesnt have any html links. I had a look at Bio::Graphics::Browser and Bio::FeatureFile and couldnt find wh ats up. Does anyone have any suggestions? I am using the most uptodate versions of all the modules in cvs and mysql yeast db. Thanks --------------------------------- Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. |
From: <ji...@dn...> - 2003-05-14 13:15:57
|
I've tried, and here is the message what I got from server error.log: "auto_find() called with cctcgacttgaggttttccgc at /usr/local/apache/conf/gbrowse.conf/plugins/OligoFinder.pm line 71." I get the exactly same message when I search for oligo in both lower and upper cases. From GBrowse, the whole message is: "The landmark named CCTCGACTTGAGGTTTTCCGC (via Short Oligos search) is not recognized. See the help pages for suggestions" Jing Lincoln Stein <lstein@cshl.o To: ji...@dn..., rg> gmo...@li... cc: 05/13/2003 Subject: Re: [Gmod-gbrowse] oligofinder problem 06:09 PM Please respond to lstein Could you put a warning into the OligoFinder.pm auto_find() subroutine and check whether the search routine is even being called? # auto_find() does the actual work # It is also called by the main page as a last resort when the user # types something into the search box that isn't recognized. sub auto_find { my $self = shift; my $oligo = lc shift; warn "auto_find() called with $oligo";^^^^^^^^^ $self->valid_oligo($oligo) or return; (my $reversec = $oligo) =~ tr/gatcGATC/ctagCTAG/; $reversec = reverse $reversec; my $length = length $oligo; ... You should see this message appear in the server error log. Lincoln On Monday 12 May 2003 05:23 am, ji...@dn... wrote: > > Do you have the OligoFinder plugin listed among the > > other plugins in your configuration file? > > Yes. I do. > > Jing > > > > > Lincoln Stein > <lstein@cshl.o To: ji...@dn..., > rg> > gmo...@li... cc: > 05/11/2003 Subject: Re: [Gmod-gbrowse] > oligofinder problem 08:39 PM > Please respond > to lstein > > > > > > > Here's a silly question. Do you have the OligoFinder plugin listed among > the > other plugins in your configuration file? > > plugins = FastaDumper > OligoFinder RestrictionAnnotator > GFFDumper GeneFinder > BatchDumper > > > Lincoln > > On Wednesday 07 May 2003 03:14 pm, ji...@dn... wrote: > > Hello, > > > > I get the same problem about OligoFinder. I am using bioperl 1.2 and I > > do > > > load sequence in my database. I've tried on both 1.49 and 1.50, with > > 21bp > > > oligo in both upper and lower cases. But I always get info as "landmark > > not recognized". > > > > Jing > > > > > > Also, the oligo-searching function doesn't work. It keeps coming up > > > > "landmark not recognized". I vaguely remember it working in the 1.49 > > > > version of GBrowse. Now I'm using v1.50 and bioperl 1.2.1. > > > > ------------------------------------------------------- > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > > The only event dedicated to issues related to Linux enterprise solutions > > www.enterpriselinuxforum.com > > > > _______________________________________________ > > Gmod-gbrowse mailing list > > Gmo...@li... > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- ======================================================================== Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs... Cold Spring Harbor, NY ======================================================================== |
From: David L. <dav...@ya...> - 2003-05-14 03:19:56
|
I finally got it working... Thanks Lincoln and Scott for your help Lincoln Stein <ls...@cs...> wrote: Hi David, Let's focus on the main gbrowse script for the moment. What queries make it stop? Does it stop with a crash, or just hang trying to fetch data? I'm thinking that if you are trying to do a keyword search, then there is a bug in some recent CVS versions of gbrowse that is fixed by updating to the very latest CVS (as of this weekend). Lincoln On Tuesday 13 May 2003 03:48 pm, David Lyon wrote: > Hello > > I am trying to implement gbrowse and I am stuck. I > have a few questions. > > I have populated a mysql with the sample data provided > > > Running the script gbrowse_img > I get the correct image return with > gbrowse_img?source=yeast;name=II > returns the overview image as seen on wormbase. > > > I get an empty image with a scale and key BUT no genes > > gbrowse_img?source=yeast;name=I > Why arent any of the features showing? > > Running gbrowse: > The web page loads OK but when I query the web page, > it loads and then stops just a point just below the > search button just at the point where the images are > suppose to appear next. > > Anyone with ideas why no images are returned with > gbrowse? > > > There are no indication of errors in web logs > Using debug =1 gives no clear indiction of an error. > dumping fasta dna sequences work from gb_browse. > > Any suggestions would be appreciated > > Cheers > > __________________________________ > Do you Yahoo!? > The New Yahoo! Search - Faster. Easier. Bingo. > http://search.yahoo.com > > > ------------------------------------------------------- > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > The only event dedicated to issues related to Linux enterprise solutions > www.enterpriselinuxforum.com > > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- ======================================================================== Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs... Cold Spring Harbor, NY ======================================================================== --------------------------------- Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. |
From: Lincoln S. <ls...@cs...> - 2003-05-13 22:10:05
|
Could you put a warning into the OligoFinder.pm auto_find() subroutine an= d=20 check whether the search routine is even being called? # auto_find() does the actual work=20 # It is also called by the main page as a last resort when the user=20 # types something into the search box that isn't recognized.=20 sub auto_find {=20 my $self =3D shift;=20 my $oligo =3D lc shift;=20 warn "auto_find() called with $oligo";^^^^^^^^^ =20 $self->valid_oligo($oligo) or return;=20 =20 (my $reversec =3D $oligo) =3D~ tr/gatcGATC/ctagCTAG/;=20 $reversec =3D reverse $reversec;=20 my $length =3D length $oligo;=20 ... You should see this message appear in the server error log. Lincoln On Monday 12 May 2003 05:23 am, ji...@dn... wrote: > > Do you have the OligoFinder plugin listed among the > > other plugins in your configuration file? > > Yes. I do. > > Jing > > > > > Lincoln Stein > <lstein@cshl.o To: ji...@dn...= , > rg> =20 > gmo...@li... cc: > 05/11/2003 Subject: Re: [Gmod-gbrowse= ] > oligofinder problem 08:39 PM > Please respond > to lstein > > > > > > > Here's a silly question. Do you have the OligoFinder plugin listed amo= ng > the > other plugins in your configuration file? > > plugins =3D FastaDumper > OligoFinder RestrictionAnnotator > GFFDumper GeneFinder > BatchDumper > > > Lincoln > > On Wednesday 07 May 2003 03:14 pm, ji...@dn... wrote: > > Hello, > > > > I get the same problem about OligoFinder. I am using bioperl 1.2 and= I > > do > > > load sequence in my database. I've tried on both 1.49 and 1.50, with > > 21bp > > > oligo in both upper and lower cases. But I always get info as "landm= ark > > not recognized". > > > > Jing > > > > > > Also, the oligo-searching function doesn't work. It keeps coming = up > > > > "landmark not recognized". I vaguely remember it working in the 1= =2E49 > > > > version of GBrowse. Now I'm using v1.50 and bioperl 1.2.1. > > > > ------------------------------------------------------- > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > > The only event dedicated to issues related to Linux enterprise soluti= ons > > www.enterpriselinuxforum.com > > > > _______________________________________________ > > Gmod-gbrowse mailing list > > Gmo...@li... > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
From: Lincoln S. <ls...@cs...> - 2003-05-13 20:32:26
|
Hi David, Let's focus on the main gbrowse script for the moment. What queries make= it=20 stop? Does it stop with a crash, or just hang trying to fetch data? I'm thinking that if you are trying to do a keyword search, then there is= a=20 bug in some recent CVS versions of gbrowse that is fixed by updating to t= he=20 very latest CVS (as of this weekend). Lincoln On Tuesday 13 May 2003 03:48 pm, David Lyon wrote: > Hello > > I am trying to implement gbrowse and I am stuck. I > have a few questions. > > I have populated a mysql with the sample data provided > > > Running the script gbrowse_img > I get the correct image return with > gbrowse_img?source=3Dyeast;name=3DII > returns the overview image as seen on wormbase. > > > I get an empty image with a scale and key BUT no genes > > gbrowse_img?source=3Dyeast;name=3DI > Why arent any of the features showing? > > Running gbrowse: > The web page loads OK but when I query the web page, > it loads and then stops just a point just below the > search button just at the point where the images are > suppose to appear next. > > Anyone with ideas why no images are returned with > gbrowse? > > > There are no indication of errors in web logs > Using debug =3D1 gives no clear indiction of an error. > dumping fasta dna sequences work from gb_browse. > > Any suggestions would be appreciated > > Cheers > > __________________________________ > Do you Yahoo!? > The New Yahoo! Search - Faster. Easier. Bingo. > http://search.yahoo.com > > > ------------------------------------------------------- > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > The only event dedicated to issues related to Linux enterprise solution= s > www.enterpriselinuxforum.com > > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
From: David L. <dav...@ya...> - 2003-05-13 19:50:02
|
Hello I am trying to implement gbrowse and I am stuck. I have a few questions. I have populated a mysql with the sample data provided Running the script gbrowse_img I get the correct image return with gbrowse_img?source=yeast;name=II returns the overview image as seen on wormbase. I get an empty image with a scale and key BUT no genes gbrowse_img?source=yeast;name=I Why arent any of the features showing? Running gbrowse: The web page loads OK but when I query the web page, it loads and then stops just a point just below the search button just at the point where the images are suppose to appear next. Anyone with ideas why no images are returned with gbrowse? There are no indication of errors in web logs Using debug =1 gives no clear indiction of an error. dumping fasta dna sequences work from gb_browse. Any suggestions would be appreciated Cheers __________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. http://search.yahoo.com |
From: Ken Y. C. <kc...@cs...> - 2003-05-12 16:40:37
|
On Mon, 12 May 2003, Shashank Bhide wrote: > Hi all, > I want to install the Gbrowse and have installed the required modules. > The perl Makefile.PL and make executes smoothly. However, when I run the > make test command, I get the following output. > Please advise.... > PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib > -I/usr/perl5/5.00503/sun4-solaris -I/usr/perl5/5.00503 -e 'use > Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t > t/01yeast...........Can't locate DBI.pm in @INC (@INC contains: t blib/arch ^^^^^^^^^^^^^^^^^^^ Shashank, You haven't installed DBI yet. ky > blib/lib /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503/sun4-solaris > /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503 > /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503/sun4-solaris > /usr/perl5/5.00503 /usr/perl5/site_perl/5.005/sun4-solaris > /usr/perl5/site_perl/5.005/sun4-solaris /usr/perl5/site_perl/5.005 . > /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503 > /usr/perl5/site_perl/5.005/sun4-solaris /usr/perl5/site_perl/5.005 .) at > t/01yeast.t line 23. > BEGIN failed--compilation aborted at t/01yeast.t line 23. > dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-7 > Failed 7/7 tests, 0.00% okay > Failed Test Status Wstat Total Fail Failed List of failed > ------------------------------------------------------------------------------- > t/01yeast.t 2 512 7 7 100.00% 1-7 > Failed 1/1 test scripts, 0.00% okay. 7/7 subtests failed, 0.00% okay. > *** Error code 2 > make: Fatal error: Command failed for target `test_dynamic' > > > Thankyou, > Shashank > > Shashank Bhide > Oklahoma State University > 405 744 7103 (Off) > 405 744 7799 (Fax) > > > > > ------------------------------------------------------- > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > The only event dedicated to issues related to Linux enterprise solutions > www.enterpriselinuxforum.com > > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > |
From: Scott C. <ca...@cs...> - 2003-05-12 16:34:38
|
Shashank, make test won't run until after the database is initialized and data is loaded in. Has that happened yet? Scott On Mon, 2003-05-12 at 12:29, Shashank Bhide wrote: > Hi all, > I want to install the Gbrowse and have installed the required modules. > The perl Makefile.PL and make executes smoothly. However, when I run the > make test command, I get the following output. > Please advise.... > PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib > -I/usr/perl5/5.00503/sun4-solaris -I/usr/perl5/5.00503 -e 'use > Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t > t/01yeast...........Can't locate DBI.pm in @INC (@INC contains: t blib/arch > blib/lib /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503/sun4-solaris > /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503 > /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503/sun4-solaris > /usr/perl5/5.00503 /usr/perl5/site_perl/5.005/sun4-solaris > /usr/perl5/site_perl/5.005/sun4-solaris /usr/perl5/site_perl/5.005 . > /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503 > /usr/perl5/site_perl/5.005/sun4-solaris /usr/perl5/site_perl/5.005 .) at > t/01yeast.t line 23. > BEGIN failed--compilation aborted at t/01yeast.t line 23. > dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-7 > Failed 7/7 tests, 0.00% okay > Failed Test Status Wstat Total Fail Failed List of failed > ------------------------------------------------------------------------------- > t/01yeast.t 2 512 7 7 100.00% 1-7 > Failed 1/1 test scripts, 0.00% okay. 7/7 subtests failed, 0.00% okay. > *** Error code 2 > make: Fatal error: Command failed for target `test_dynamic' > > > Thankyou, > Shashank > > Shashank Bhide > Oklahoma State University > 405 744 7103 (Off) > 405 744 7799 (Fax) > > > > > ------------------------------------------------------- > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > The only event dedicated to issues related to Linux enterprise solutions > www.enterpriselinuxforum.com > > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
From: Shashank B. <sha...@bi...> - 2003-05-12 16:27:22
|
Hi all, I want to install the Gbrowse and have installed the required modules. The perl Makefile.PL and make executes smoothly. However, when I run the make test command, I get the following output. Please advise.... PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/perl5/5.00503/sun4-solaris -I/usr/perl5/5.00503 -e 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t t/01yeast...........Can't locate DBI.pm in @INC (@INC contains: t blib/arch blib/lib /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503 /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503 /usr/perl5/site_perl/5.005/sun4-solaris /usr/perl5/site_perl/5.005/sun4-solaris /usr/perl5/site_perl/5.005 . /usr/perl5/5.00503/sun4-solaris /usr/perl5/5.00503 /usr/perl5/site_perl/5.005/sun4-solaris /usr/perl5/site_perl/5.005 .) at t/01yeast.t line 23. BEGIN failed--compilation aborted at t/01yeast.t line 23. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-7 Failed 7/7 tests, 0.00% okay Failed Test Status Wstat Total Fail Failed List of failed ------------------------------------------------------------------------------- t/01yeast.t 2 512 7 7 100.00% 1-7 Failed 1/1 test scripts, 0.00% okay. 7/7 subtests failed, 0.00% okay. *** Error code 2 make: Fatal error: Command failed for target `test_dynamic' Thankyou, Shashank Shashank Bhide Oklahoma State University 405 744 7103 (Off) 405 744 7799 (Fax) |
From: <ji...@dn...> - 2003-05-12 09:10:43
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> Do you have the OligoFinder plugin listed among the > other plugins in your configuration file? Yes. I do. Jing Lincoln Stein <lstein@cshl.o To: ji...@dn..., rg> gmo...@li... cc: 05/11/2003 Subject: Re: [Gmod-gbrowse] oligofinder problem 08:39 PM Please respond to lstein Here's a silly question. Do you have the OligoFinder plugin listed among the other plugins in your configuration file? plugins = FastaDumper OligoFinder RestrictionAnnotator GFFDumper GeneFinder BatchDumper Lincoln On Wednesday 07 May 2003 03:14 pm, ji...@dn... wrote: > Hello, > > I get the same problem about OligoFinder. I am using bioperl 1.2 and I do > load sequence in my database. I've tried on both 1.49 and 1.50, with 21bp > oligo in both upper and lower cases. But I always get info as "landmark > not recognized". > > Jing > > > > Also, the oligo-searching function doesn't work. It keeps coming up > > > "landmark not recognized". I vaguely remember it working in the 1.49 > > > version of GBrowse. Now I'm using v1.50 and bioperl 1.2.1. > > ------------------------------------------------------- > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara > The only event dedicated to issues related to Linux enterprise solutions > www.enterpriselinuxforum.com > > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Lincoln Stein ls...@cs... Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) |