no regions are shown :-(

[Lincoln Stein-3]

Hi Erick,


The problem with the karyotype display is now resolved. The fix is in GBrowse CVS and will go into CPAN over the weekend.

Lincoln

On Fri, May 29, 2009 at 2:37 PM, Lincoln Stein <lincoln.stein@...> wrote:

Hi Erick,

I've reproduced the crash and am working on it.

Lincoln

On Fri, May 29, 2009 at 8:51 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

have you been able to reproduce the scenario? Please let me know if you need some more info,

thanks
erick

2009/5/27 Erick Antezana <erick.antezana@...>

Hi Lincoln,

  please find below the log corresponding to scenario B (the new warning was added):

[error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 213 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  about to draw seqid = 3635_AAA12622 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 123.,
 [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 125.,
 [error]  about to draw seqid = 3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 123.,


  the lines in my GFF3 are the following:

##gff-version 3
#DATE: 11-27-2008_12:28:52

#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes

3635_AAA12622   TEST   sequence        1       3710    .       +       .       ID=3635_AAA12622;Note=BAC sequence containing the gluc3-GhD genes
3635_AAA12622   RepeatMasker_REPEAT_Repbase     repeat_region   2767    3709     6.4    +       .       ID=3635_AAA12622.repeat.736803216
3635_AAA12622   RepeatMasker_REPEAT_Repbase     repeat_region   1       640      8.9    +       .       ID=3635_AAA12622.repeat.766729817

##gff-version 3
#DATE: 11-27-2008_12:42:53

#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes

3635_AAA12625   TEST   sequence        1       7708    .       +       .       ID=3635_AAA12625;Note=BAC sequence containing the gluc3-GhD genes
3635_AAA12625   TERA-RepeatMasker_REPEAT_Repbase   repeat_region       351     533     1.7E-15 +       .       ID=A2Q169_MEDTR_062509

thanks,
Erick

2009/5/27 Lincoln Stein <lincoln.stein@...>

Hi Erick,

One of the BACs (the second one it tires to draw) is triggering the crash in scenario B. The last bit of debugging I need for you to do is to insert the following warnings before line 122, where the call to generate_image() occurs:

 warn "about to draw seqid = $seqid";

Then send me the line in your GFF3 file that describes this BAC. I will try to reproduce and fix the problem.

Lincoln

On Wed, May 27, 2009 at 4:15 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

  we have tested three different scenarios (A, B, C) for which you can see their corresponding error logs:

(A)

* Karyotype.pm file = original version used (warnings added as you had suggested)
* 15 regions should be shown
* result: it works (i.e. it shows correctly the images, table, etc.)
* the log is:

[Wed May 27 09:50:41 2009] [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),
[Wed May 27 09:50:41 2009] [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
[Wed May 27 09:50:41 2009] [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 124.,

(B)

* Karyotype.pm file = original version used (warnings added as you had suggested)
* 800 regions should be shown
* result: it does not work
* the log is:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 212 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 124.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,


(C)

* Karyotype.pm file = original version used (warnings added as you had suggested AND SUPPRESS_SMALL_CHROMOSOMES => 50000000;)
* 800 regions should be shown (same as in case B)
* result: it partially works: table is propertly shown but images (karyotype display) is off (as expected).
* the log is:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 212 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  Use of uninitialized value $html in concatenation (.) or string at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 143 (#2),
 [error]      (W uninitialized) An undefined value was used as if it were already,
 [error]      defined.  It was interpreted as a "" or a 0, but maybe it was a mistake.,
 [error]      To suppress this warning assign a defined value to your variables.,
 [error]      ,
 [error]      To help you figure out what was undefined, perl will try to tell you the,
 [error]      name of the variable (if any) that was undefined. In some cases it cannot,
 [error]      do this, so it also tells you what operation you used the undefined value,
 [error]      in.  Note, however, that perl optimizes your program and the operation,
 [error]      displayed in the warning may not necessarily appear literally in your,
 [error]      program.  For example, "that $foo" is usually optimized into "that ",
 [error]      . $foo, and the warning will refer to the concatenation (.) operator,,
 [error]      even though there is no . in your program.,

cheers,
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

To turn off the karyotype display temporarily so that you can get a text table of the results, please find Bio/Graphics/Karyotype.pm and edit the following line to give it a very large value:

 use constant SUPPRESS_SMALL_CHROMOSOMES => 50;

change to

use constant SUPPRESS_SMALL_CHROMOSOMES => 50000000;

while you're at it, find line 122, which reads

my $url    = $source->generate_image($panel->gd);

and put warnings above and below it like so:

warn "about to draw image";
my $url    = $source->generate_image($panel->gd);
warn "drew image";

This will tell me whether the crash is actually occurring where I think it is.

Lincoln

On Tue, May 26, 2009 at 3:09 PM, Lincoln Stein <lincoln.stein@...> wrote:

Any luck when you change the height or width of the chromosomes?

Lincoln

On Tue, May 26, 2009 at 3:07 PM, Erick Antezana <erick.antezana@...> wrote:

Hi,

yes, the karyotype display is not working with the yeast sample data source.

Erick

---------- Forwarded message ----------
From: Lincoln Stein <lincoln.stein@...>
Date: 2009/5/26
Subject: Re: [Gmod-gbrowse] no regions are shown :-(
To: Erick Antezana <erick.antezana@...>
Cc: "gmod-gbrowse@..." <gmod-gbrowse@...>


Hi Erick,

The karyotype display is not working with the yeast sample data source either, right?

I may have to provide a way to disable the karyotype display until I can get to the bottom of this.

Lincoln

On Tue, May 26, 2009 at 11:57 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

that feature comes from a DB with about 1300 sequences (BACs). Here you are an excerpt of the GFF3 file:

##gff-version 3
#DATE: 11-27-2008_15:24:52
#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes
3635_AAA12620   TEST   sequence        1       10680   .       +       .       ID=3635_AAA12620;Note=BAC sequence containing apex gene
3635_AAA12620   Unigene match_set       404     700     3.2E-32 +       .       ID=3633R_pc3837_c1_081870
3635_AAA12620   Unigene match_part      404     700     3.2E-32 +       .       Parent=3633R_pc3837_c1_081870

if I search over the Yeast sample data source (Yeast chromosomes 1+2), I only get:

 n1=chrI, n2=chrII at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.

I do not get the other errors (numeric comparison, etc) as with the BACs

cheers,
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

This is unexpected. I was expecting a small number of chromosome names. What type of feature is 3635_AAA12621?

Lincoln

On Tue, May 26, 2009 at 11:17 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

Here is the new excerpt (after adding the warnings):

[error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 210 (#1),
 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,

 [error]      ,
 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,

cheers,

Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

This error may indicate some problem unrelated to libgd. Could you do me a favor and insert the following diagnostic message into line 206 of Karyotype.pm (easiest to do it directly in /usr/local/lib/perl5/site_perl...), and then send me the error log output?

 warn "n1=$n1, n2=$n2";

Thanks,

Lincoln

On Tue, May 26, 2009 at 10:47 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

I have just installed libgd 2.0.36RC1 and the problem is still there (I checked that I do not need to recompile GD; thanks for the ldd tip!).

here is an excerpt of my apache error log file:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),
 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 210 (#1),
 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,

thanks again,

Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

You said:

the problem is still there although now the apache error log is more informative

What do you see in the error log?

Perhaps this isn't the libgd bug at all but something different. That would be a relief to me.

inkscape doesn't use libgd, so you don't have to worry about that. You only need to recompile GD if it is linked to libgd dynamically. The way to do this is to find GD.so, and then:

% ldd /usr/lib/perl5/auto/GD/GD.so
    linux-gate.so.1 =>  (0xb809b000)
    libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0xb802e000)
    libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb7fb7000)
    libpng12.so.0 => /usr/lib/libpng12.so.0 (0xb7f90000)
    libz.so.1 => /lib/libz.so.1 (0xb7f7a000)
    libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7f54000)
    libgd.so.2 => /usr/lib/libgd.so.2 (0xb7f13000)
    libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7db0000)
    /lib/ld-linux.so.2 (0xb809c000)

This shows that my version of GD is dynamically linked and doesn't need to be recompiled.

Lincoln

On Tue, May 26, 2009 at 10:14 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

 I forgot to mention that I am not getting the "child process terminated" in my error log...

 on the other hand, do I need to recompile any other package apart from GD? perhaps inkscape?

thanks
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

Are you getting the "child process terminated" error in your apache log?

I am using GD version 2.39 without getting crashes, but the GD version is not related to the crash, as it occurs deep in libgd. However, after installing the new libgd, you may need to recompile GD.

Also, try adjusting the appearance of the karyotype:

 [builtin:karyotype]
 chrom_width  =  20
 chrom_height = 150

and variants of the above.

I had thought this problem was fixed, but apparently I need to do some more work.

Lincoln

On Tue, May 26, 2009 at 9:25 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

 Our system had 2.0.33, we have just installed the lastest release (2.0.35) but the problem is still there although now the apache error log is more informative.... I have checked on the libgd site (http://www.libgd.org/Downloads) that the latest release is 2.0.35 but there is also a candidate release (2.0.36RC1) as well as a develompent one (2.1.0.-dev).  which version of GD would you recommend to use? (I have Bio::Graphics version 1.94)

thanks,
Erick

2009/5/25 Lincoln Stein <lincoln.stein@...>

Hi Erick,

There is a persistent bug in libgd that the karyotype display (used to show multiple hits; see enclosed) somehow triggers. Usually you will see a "child process unexpectedly terminated" in one of your apache logs -- if you are using virtual hosts, then it will be in the main error log, and not in the virutal host one.

Here are steps to try to fix the problem:

1. Install the latest Bio::Graphics from CPAN. It contains code that works around the problem.
2. Recompile libgd from the latest source.
3. Complain to me if you try (1) and (2) and the problem persists.

Lincoln

On Mon, May 25, 2009 at 11:21 AM, Erick Antezana <erick.antezana@...> wrote:

Hi,

  Our local installation of GBrowse 2.0 was successfully installed some days ago and we were testing the "Search" capabilities on specific regions and landmarks. If we look for a particular region, GBrowse is able to find it and show it. However, we got some problems to find a landmark (free text): if we use for instance the sample data source "Yeast chromosomes 1+2 (basic)" and we look for "membrane trafficking", the server shows on the top:

Yeast chromosomes 1+2 (basic): The following 66 regions match your request.

However, no region is shown below. I have checked on the Apache error log file, and there is no message. We have also tried the "Search" functionality out with our internal data and the behaviour is identical. Any suggestions?

cheers,
Erick

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://www.creativitycat.com
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Erick Antezana-4]

Hi Lincoln,

 yes, indeed, the problem is gone.

thanks again!
Erick

2009/5/29 Lincoln Stein <lincoln.stein@...>

Hi Erick,


The problem with the karyotype display is now resolved. The fix is in GBrowse CVS and will go into CPAN over the weekend.

Lincoln

On Fri, May 29, 2009 at 2:37 PM, Lincoln Stein <lincoln.stein@...> wrote:

Hi Erick,

I've reproduced the crash and am working on it.

Lincoln

On Fri, May 29, 2009 at 8:51 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

have you been able to reproduce the scenario? Please let me know if you need some more info,

thanks
erick

2009/5/27 Erick Antezana <erick.antezana@...>

Hi Lincoln,

  please find below the log corresponding to scenario B (the new warning was added):

[error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 213 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  about to draw seqid = 3635_AAA12622 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 123.,
 [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 125.,
 [error]  about to draw seqid = 3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 123.,


  the lines in my GFF3 are the following:

##gff-version 3
#DATE: 11-27-2008_12:28:52

#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes

3635_AAA12622   TEST   sequence        1       3710    .       +       .       ID=3635_AAA12622;Note=BAC sequence containing the gluc3-GhD genes
3635_AAA12622   RepeatMasker_REPEAT_Repbase     repeat_region   2767    3709     6.4    +       .       ID=3635_AAA12622.repeat.736803216
3635_AAA12622   RepeatMasker_REPEAT_Repbase     repeat_region   1       640      8.9    +       .       ID=3635_AAA12622.repeat.766729817

##gff-version 3
#DATE: 11-27-2008_12:42:53

#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes

3635_AAA12625   TEST   sequence        1       7708    .       +       .       ID=3635_AAA12625;Note=BAC sequence containing the gluc3-GhD genes
3635_AAA12625   TERA-RepeatMasker_REPEAT_Repbase   repeat_region       351     533     1.7E-15 +       .       ID=A2Q169_MEDTR_062509

thanks,
Erick

2009/5/27 Lincoln Stein <lincoln.stein@...>

Hi Erick,

One of the BACs (the second one it tires to draw) is triggering the crash in scenario B. The last bit of debugging I need for you to do is to insert the following warnings before line 122, where the call to generate_image() occurs:

 warn "about to draw seqid = $seqid";

Then send me the line in your GFF3 file that describes this BAC. I will try to reproduce and fix the problem.

Lincoln

On Wed, May 27, 2009 at 4:15 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

  we have tested three different scenarios (A, B, C) for which you can see their corresponding error logs:

(A)

* Karyotype.pm file = original version used (warnings added as you had suggested)
* 15 regions should be shown
* result: it works (i.e. it shows correctly the images, table, etc.)
* the log is:

[Wed May 27 09:50:41 2009] [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),
[Wed May 27 09:50:41 2009] [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
[Wed May 27 09:50:41 2009] [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 124.,

(B)

* Karyotype.pm file = original version used (warnings added as you had suggested)
* 800 regions should be shown
* result: it does not work
* the log is:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 212 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 124.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,


(C)

* Karyotype.pm file = original version used (warnings added as you had suggested AND SUPPRESS_SMALL_CHROMOSOMES => 50000000;)
* 800 regions should be shown (same as in case B)
* result: it partially works: table is propertly shown but images (karyotype display) is off (as expected).
* the log is:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 212 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  Use of uninitialized value $html in concatenation (.) or string at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 143 (#2),
 [error]      (W uninitialized) An undefined value was used as if it were already,
 [error]      defined.  It was interpreted as a "" or a 0, but maybe it was a mistake.,
 [error]      To suppress this warning assign a defined value to your variables.,
 [error]      ,
 [error]      To help you figure out what was undefined, perl will try to tell you the,
 [error]      name of the variable (if any) that was undefined. In some cases it cannot,
 [error]      do this, so it also tells you what operation you used the undefined value,
 [error]      in.  Note, however, that perl optimizes your program and the operation,
 [error]      displayed in the warning may not necessarily appear literally in your,
 [error]      program.  For example, "that $foo" is usually optimized into "that ",
 [error]      . $foo, and the warning will refer to the concatenation (.) operator,,
 [error]      even though there is no . in your program.,

cheers,
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

To turn off the karyotype display temporarily so that you can get a text table of the results, please find Bio/Graphics/Karyotype.pm and edit the following line to give it a very large value:

 use constant SUPPRESS_SMALL_CHROMOSOMES => 50;

change to

use constant SUPPRESS_SMALL_CHROMOSOMES => 50000000;

while you're at it, find line 122, which reads

my $url    = $source->generate_image($panel->gd);

and put warnings above and below it like so:

warn "about to draw image";
my $url    = $source->generate_image($panel->gd);
warn "drew image";

This will tell me whether the crash is actually occurring where I think it is.

Lincoln

On Tue, May 26, 2009 at 3:09 PM, Lincoln Stein <lincoln.stein@...> wrote:

Any luck when you change the height or width of the chromosomes?

Lincoln

On Tue, May 26, 2009 at 3:07 PM, Erick Antezana <erick.antezana@...> wrote:

Hi,

yes, the karyotype display is not working with the yeast sample data source.

Erick

---------- Forwarded message ----------
From: Lincoln Stein <lincoln.stein@...>
Date: 2009/5/26
Subject: Re: [Gmod-gbrowse] no regions are shown :-(
To: Erick Antezana <erick.antezana@...>
Cc: "gmod-gbrowse@..." <gmod-gbrowse@...>


Hi Erick,

The karyotype display is not working with the yeast sample data source either, right?

I may have to provide a way to disable the karyotype display until I can get to the bottom of this.

Lincoln

On Tue, May 26, 2009 at 11:57 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

that feature comes from a DB with about 1300 sequences (BACs). Here you are an excerpt of the GFF3 file:

##gff-version 3
#DATE: 11-27-2008_15:24:52
#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes
3635_AAA12620   TEST   sequence        1       10680   .       +       .       ID=3635_AAA12620;Note=BAC sequence containing apex gene
3635_AAA12620   Unigene match_set       404     700     3.2E-32 +       .       ID=3633R_pc3837_c1_081870
3635_AAA12620   Unigene match_part      404     700     3.2E-32 +       .       Parent=3633R_pc3837_c1_081870

if I search over the Yeast sample data source (Yeast chromosomes 1+2), I only get:

 n1=chrI, n2=chrII at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.

I do not get the other errors (numeric comparison, etc) as with the BACs

cheers,
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

This is unexpected. I was expecting a small number of chromosome names. What type of feature is 3635_AAA12621?

Lincoln

On Tue, May 26, 2009 at 11:17 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

Here is the new excerpt (after adding the warnings):

[error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 210 (#1),
 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,

 [error]      ,
 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,

cheers,

Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

This error may indicate some problem unrelated to libgd. Could you do me a favor and insert the following diagnostic message into line 206 of Karyotype.pm (easiest to do it directly in /usr/local/lib/perl5/site_perl...), and then send me the error log output?

 warn "n1=$n1, n2=$n2";

Thanks,

Lincoln

On Tue, May 26, 2009 at 10:47 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

I have just installed libgd 2.0.36RC1 and the problem is still there (I checked that I do not need to recompile GD; thanks for the ldd tip!).

here is an excerpt of my apache error log file:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),
 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 210 (#1),
 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,

thanks again,

Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

You said:

the problem is still there although now the apache error log is more informative

What do you see in the error log?

Perhaps this isn't the libgd bug at all but something different. That would be a relief to me.

inkscape doesn't use libgd, so you don't have to worry about that. You only need to recompile GD if it is linked to libgd dynamically. The way to do this is to find GD.so, and then:

% ldd /usr/lib/perl5/auto/GD/GD.so
    linux-gate.so.1 =>  (0xb809b000)
    libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0xb802e000)
    libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb7fb7000)
    libpng12.so.0 => /usr/lib/libpng12.so.0 (0xb7f90000)
    libz.so.1 => /lib/libz.so.1 (0xb7f7a000)
    libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7f54000)
    libgd.so.2 => /usr/lib/libgd.so.2 (0xb7f13000)
    libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7db0000)
    /lib/ld-linux.so.2 (0xb809c000)

This shows that my version of GD is dynamically linked and doesn't need to be recompiled.

Lincoln

On Tue, May 26, 2009 at 10:14 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

 I forgot to mention that I am not getting the "child process terminated" in my error log...

 on the other hand, do I need to recompile any other package apart from GD? perhaps inkscape?

thanks
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

Are you getting the "child process terminated" error in your apache log?

I am using GD version 2.39 without getting crashes, but the GD version is not related to the crash, as it occurs deep in libgd. However, after installing the new libgd, you may need to recompile GD.

Also, try adjusting the appearance of the karyotype:

 [builtin:karyotype]
 chrom_width  =  20
 chrom_height = 150

and variants of the above.

I had thought this problem was fixed, but apparently I need to do some more work.

Lincoln

On Tue, May 26, 2009 at 9:25 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

 Our system had 2.0.33, we have just installed the lastest release (2.0.35) but the problem is still there although now the apache error log is more informative.... I have checked on the libgd site (http://www.libgd.org/Downloads) that the latest release is 2.0.35 but there is also a candidate release (2.0.36RC1) as well as a develompent one (2.1.0.-dev).  which version of GD would you recommend to use? (I have Bio::Graphics version 1.94)

thanks,
Erick

2009/5/25 Lincoln Stein <lincoln.stein@...>

Hi Erick,

There is a persistent bug in libgd that the karyotype display (used to show multiple hits; see enclosed) somehow triggers. Usually you will see a "child process unexpectedly terminated" in one of your apache logs -- if you are using virtual hosts, then it will be in the main error log, and not in the virutal host one.

Here are steps to try to fix the problem:

1. Install the latest Bio::Graphics from CPAN. It contains code that works around the problem.
2. Recompile libgd from the latest source.
3. Complain to me if you try (1) and (2) and the problem persists.

Lincoln

On Mon, May 25, 2009 at 11:21 AM, Erick Antezana <erick.antezana@...> wrote:

Hi,

  Our local installation of GBrowse 2.0 was successfully installed some days ago and we were testing the "Search" capabilities on specific regions and landmarks. If we look for a particular region, GBrowse is able to find it and show it. However, we got some problems to find a landmark (free text): if we use for instance the sample data source "Yeast chromosomes 1+2 (basic)" and we look for "membrane trafficking", the server shows on the top:

Yeast chromosomes 1+2 (basic): The following 66 regions match your request.

However, no region is shown below. I have checked on the Apache error log file, and there is no message. We have also tried the "Search" functionality out with our internal data and the behaviour is identical. Any suggestions?

cheers,
Erick

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://www.creativitycat.com
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Erick Antezana-4]

Hi again,

I am afraid to tell you that this problem seems to still be there while searching for results with many more regions, the error message is:

 [error]  Odd number of elements in hash assignment at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/PluginSet.pm line 197 (#1),
 [error]      (W misc) You specified an odd number of elements to initialize a hash,,
 [error]      which is odd, because hashes come in key/value pairs.,
 [error]      ,
 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 213 (#2),
 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,

Now, it is possible to retrieve (search for) some of the regions that previously were not possible...

Erick

2009/6/2 Erick Antezana <erick.antezana@...>

Hi Lincoln,

 yes, indeed, the problem is gone.

thanks again!
Erick

2009/5/29 Lincoln Stein <lincoln.stein@...>

Hi Erick,


The problem with the karyotype display is now resolved. The fix is in GBrowse CVS and will go into CPAN over the weekend.

Lincoln

On Fri, May 29, 2009 at 2:37 PM, Lincoln Stein <lincoln.stein@...> wrote:

Hi Erick,

I've reproduced the crash and am working on it.

Lincoln

On Fri, May 29, 2009 at 8:51 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

have you been able to reproduce the scenario? Please let me know if you need some more info,

thanks
erick

2009/5/27 Erick Antezana <erick.antezana@...>

Hi Lincoln,

  please find below the log corresponding to scenario B (the new warning was added):

[error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 213 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  about to draw seqid = 3635_AAA12622 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 123.,
 [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 125.,
 [error]  about to draw seqid = 3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 123.,


  the lines in my GFF3 are the following:

##gff-version 3
#DATE: 11-27-2008_12:28:52

#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes

3635_AAA12622   TEST   sequence        1       3710    .       +       .       ID=3635_AAA12622;Note=BAC sequence containing the gluc3-GhD genes
3635_AAA12622   RepeatMasker_REPEAT_Repbase     repeat_region   2767    3709     6.4    +       .       ID=3635_AAA12622.repeat.736803216
3635_AAA12622   RepeatMasker_REPEAT_Repbase     repeat_region   1       640      8.9    +       .       ID=3635_AAA12622.repeat.766729817

##gff-version 3
#DATE: 11-27-2008_12:42:53

#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes

3635_AAA12625   TEST   sequence        1       7708    .       +       .       ID=3635_AAA12625;Note=BAC sequence containing the gluc3-GhD genes
3635_AAA12625   TERA-RepeatMasker_REPEAT_Repbase   repeat_region       351     533     1.7E-15 +       .       ID=A2Q169_MEDTR_062509

thanks,
Erick

2009/5/27 Lincoln Stein <lincoln.stein@...>

Hi Erick,

One of the BACs (the second one it tires to draw) is triggering the crash in scenario B. The last bit of debugging I need for you to do is to insert the following warnings before line 122, where the call to generate_image() occurs:

 warn "about to draw seqid = $seqid";

Then send me the line in your GFF3 file that describes this BAC. I will try to reproduce and fix the problem.

Lincoln

On Wed, May 27, 2009 at 4:15 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

  we have tested three different scenarios (A, B, C) for which you can see their corresponding error logs:

(A)

* Karyotype.pm file = original version used (warnings added as you had suggested)
* 15 regions should be shown
* result: it works (i.e. it shows correctly the images, table, etc.)
* the log is:

[Wed May 27 09:50:41 2009] [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),
[Wed May 27 09:50:41 2009] [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
[Wed May 27 09:50:41 2009] [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 124.,

(B)

* Karyotype.pm file = original version used (warnings added as you had suggested)
* 800 regions should be shown
* result: it does not work
* the log is:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 212 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 124.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,


(C)

* Karyotype.pm file = original version used (warnings added as you had suggested AND SUPPRESS_SMALL_CHROMOSOMES => 50000000;)
* 800 regions should be shown (same as in case B)
* result: it partially works: table is propertly shown but images (karyotype display) is off (as expected).
* the log is:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 212 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  Use of uninitialized value $html in concatenation (.) or string at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 143 (#2),
 [error]      (W uninitialized) An undefined value was used as if it were already,
 [error]      defined.  It was interpreted as a "" or a 0, but maybe it was a mistake.,
 [error]      To suppress this warning assign a defined value to your variables.,
 [error]      ,
 [error]      To help you figure out what was undefined, perl will try to tell you the,
 [error]      name of the variable (if any) that was undefined. In some cases it cannot,
 [error]      do this, so it also tells you what operation you used the undefined value,
 [error]      in.  Note, however, that perl optimizes your program and the operation,
 [error]      displayed in the warning may not necessarily appear literally in your,
 [error]      program.  For example, "that $foo" is usually optimized into "that ",
 [error]      . $foo, and the warning will refer to the concatenation (.) operator,,
 [error]      even though there is no . in your program.,

cheers,
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

To turn off the karyotype display temporarily so that you can get a text table of the results, please find Bio/Graphics/Karyotype.pm and edit the following line to give it a very large value:

 use constant SUPPRESS_SMALL_CHROMOSOMES => 50;

change to

use constant SUPPRESS_SMALL_CHROMOSOMES => 50000000;

while you're at it, find line 122, which reads

my $url    = $source->generate_image($panel->gd);

and put warnings above and below it like so:

warn "about to draw image";
my $url    = $source->generate_image($panel->gd);
warn "drew image";

This will tell me whether the crash is actually occurring where I think it is.

Lincoln

On Tue, May 26, 2009 at 3:09 PM, Lincoln Stein <lincoln.stein@...> wrote:

Any luck when you change the height or width of the chromosomes?

Lincoln

On Tue, May 26, 2009 at 3:07 PM, Erick Antezana <erick.antezana@...> wrote:

Hi,

yes, the karyotype display is not working with the yeast sample data source.

Erick

---------- Forwarded message ----------
From: Lincoln Stein <lincoln.stein@...>
Date: 2009/5/26
Subject: Re: [Gmod-gbrowse] no regions are shown :-(
To: Erick Antezana <erick.antezana@...>
Cc: "gmod-gbrowse@..." <gmod-gbrowse@...>


Hi Erick,

The karyotype display is not working with the yeast sample data source either, right?

I may have to provide a way to disable the karyotype display until I can get to the bottom of this.

Lincoln

On Tue, May 26, 2009 at 11:57 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

that feature comes from a DB with about 1300 sequences (BACs). Here you are an excerpt of the GFF3 file:

##gff-version 3
#DATE: 11-27-2008_15:24:52
#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes
3635_AAA12620   TEST   sequence        1       10680   .       +       .       ID=3635_AAA12620;Note=BAC sequence containing apex gene
3635_AAA12620   Unigene match_set       404     700     3.2E-32 +       .       ID=3633R_pc3837_c1_081870
3635_AAA12620   Unigene match_part      404     700     3.2E-32 +       .       Parent=3633R_pc3837_c1_081870

if I search over the Yeast sample data source (Yeast chromosomes 1+2), I only get:

 n1=chrI, n2=chrII at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.

I do not get the other errors (numeric comparison, etc) as with the BACs

cheers,
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

This is unexpected. I was expecting a small number of chromosome names. What type of feature is 3635_AAA12621?

Lincoln

On Tue, May 26, 2009 at 11:17 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

Here is the new excerpt (after adding the warnings):

[error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 210 (#1),
 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,

 [error]      ,
 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,

cheers,

Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

This error may indicate some problem unrelated to libgd. Could you do me a favor and insert the following diagnostic message into line 206 of Karyotype.pm (easiest to do it directly in /usr/local/lib/perl5/site_perl...), and then send me the error log output?

 warn "n1=$n1, n2=$n2";

Thanks,

Lincoln

On Tue, May 26, 2009 at 10:47 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

I have just installed libgd 2.0.36RC1 and the problem is still there (I checked that I do not need to recompile GD; thanks for the ldd tip!).

here is an excerpt of my apache error log file:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),
 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 210 (#1),
 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,

thanks again,

Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

You said:

the problem is still there although now the apache error log is more informative

What do you see in the error log?

Perhaps this isn't the libgd bug at all but something different. That would be a relief to me.

inkscape doesn't use libgd, so you don't have to worry about that. You only need to recompile GD if it is linked to libgd dynamically. The way to do this is to find GD.so, and then:

% ldd /usr/lib/perl5/auto/GD/GD.so
    linux-gate.so.1 =>  (0xb809b000)
    libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0xb802e000)
    libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb7fb7000)
    libpng12.so.0 => /usr/lib/libpng12.so.0 (0xb7f90000)
    libz.so.1 => /lib/libz.so.1 (0xb7f7a000)
    libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7f54000)
    libgd.so.2 => /usr/lib/libgd.so.2 (0xb7f13000)
    libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7db0000)
    /lib/ld-linux.so.2 (0xb809c000)

This shows that my version of GD is dynamically linked and doesn't need to be recompiled.

Lincoln

On Tue, May 26, 2009 at 10:14 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

 I forgot to mention that I am not getting the "child process terminated" in my error log...

 on the other hand, do I need to recompile any other package apart from GD? perhaps inkscape?

thanks
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

Are you getting the "child process terminated" error in your apache log?

I am using GD version 2.39 without getting crashes, but the GD version is not related to the crash, as it occurs deep in libgd. However, after installing the new libgd, you may need to recompile GD.

Also, try adjusting the appearance of the karyotype:

 [builtin:karyotype]
 chrom_width  =  20
 chrom_height = 150

and variants of the above.

I had thought this problem was fixed, but apparently I need to do some more work.

Lincoln

On Tue, May 26, 2009 at 9:25 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

 Our system had 2.0.33, we have just installed the lastest release (2.0.35) but the problem is still there although now the apache error log is more informative.... I have checked on the libgd site (http://www.libgd.org/Downloads) that the latest release is 2.0.35 but there is also a candidate release (2.0.36RC1) as well as a develompent one (2.1.0.-dev).  which version of GD would you recommend to use? (I have Bio::Graphics version 1.94)

thanks,
Erick

2009/5/25 Lincoln Stein <lincoln.stein@...>

Hi Erick,

There is a persistent bug in libgd that the karyotype display (used to show multiple hits; see enclosed) somehow triggers. Usually you will see a "child process unexpectedly terminated" in one of your apache logs -- if you are using virtual hosts, then it will be in the main error log, and not in the virutal host one.

Here are steps to try to fix the problem:

1. Install the latest Bio::Graphics from CPAN. It contains code that works around the problem.
2. Recompile libgd from the latest source.
3. Complain to me if you try (1) and (2) and the problem persists.

Lincoln

On Mon, May 25, 2009 at 11:21 AM, Erick Antezana <erick.antezana@...> wrote:

Hi,

  Our local installation of GBrowse 2.0 was successfully installed some days ago and we were testing the "Search" capabilities on specific regions and landmarks. If we look for a particular region, GBrowse is able to find it and show it. However, we got some problems to find a landmark (free text): if we use for instance the sample data source "Yeast chromosomes 1+2 (basic)" and we look for "membrane trafficking", the server shows on the top:

Yeast chromosomes 1+2 (basic): The following 66 regions match your request.

However, no region is shown below. I have checked on the Apache error log file, and there is no message. We have also tried the "Search" functionality out with our internal data and the behaviour is identical. Any suggestions?

cheers,
Erick

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://www.creativitycat.com
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

[Lincoln Stein-3]

Ok, back to work on it.

Lincoln

On Tue, Jun 2, 2009 at 11:33 AM, Erick Antezana <erick.antezana@...> wrote:

Hi again,

I am afraid to tell you that this problem seems to still be there while searching for results with many more regions, the error message is:

 [error]  Odd number of elements in hash assignment at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Browser/PluginSet.pm line 197 (#1),
 [error]      (W misc) You specified an odd number of elements to initialize a hash,,
 [error]      which is odd, because hashes come in key/value pairs.,
 [error]      ,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 213 (#2),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,

Now, it is possible to retrieve (search for) some of the regions that previously were not possible...

Erick

2009/6/2 Erick Antezana <erick.antezana@...>

Hi Lincoln,

 yes, indeed, the problem is gone.

thanks again!
Erick

2009/5/29 Lincoln Stein <lincoln.stein@...>

Hi Erick,


The problem with the karyotype display is now resolved. The fix is in GBrowse CVS and will go into CPAN over the weekend.

Lincoln

On Fri, May 29, 2009 at 2:37 PM, Lincoln Stein <lincoln.stein@...> wrote:

Hi Erick,

I've reproduced the crash and am working on it.

Lincoln

On Fri, May 29, 2009 at 8:51 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

have you been able to reproduce the scenario? Please let me know if you need some more info,

thanks
erick

2009/5/27 Erick Antezana <erick.antezana@...>

Hi Lincoln,

  please find below the log corresponding to scenario B (the new warning was added):

[error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 213 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 209.,
 [error]  about to draw seqid = 3635_AAA12622 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 123.,
 [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 125.,
 [error]  about to draw seqid = 3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 123.,


  the lines in my GFF3 are the following:

##gff-version 3
#DATE: 11-27-2008_12:28:52

#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes

3635_AAA12622   TEST   sequence        1       3710    .       +       .       ID=3635_AAA12622;Note=BAC sequence containing the gluc3-GhD genes
3635_AAA12622   RepeatMasker_REPEAT_Repbase     repeat_region   2767    3709     6.4    +       .       ID=3635_AAA12622.repeat.736803216
3635_AAA12622   RepeatMasker_REPEAT_Repbase     repeat_region   1       640      8.9    +       .       ID=3635_AAA12622.repeat.766729817

##gff-version 3
#DATE: 11-27-2008_12:42:53

#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes

3635_AAA12625   TEST   sequence        1       7708    .       +       .       ID=3635_AAA12625;Note=BAC sequence containing the gluc3-GhD genes
3635_AAA12625   TERA-RepeatMasker_REPEAT_Repbase   repeat_region       351     533     1.7E-15 +       .       ID=A2Q169_MEDTR_062509

thanks,
Erick

2009/5/27 Lincoln Stein <lincoln.stein@...>

Hi Erick,

One of the BACs (the second one it tires to draw) is triggering the crash in scenario B. The last bit of debugging I need for you to do is to insert the following warnings before line 122, where the call to generate_image() occurs:

 warn "about to draw seqid = $seqid";

Then send me the line in your GFF3 file that describes this BAC. I will try to reproduce and fix the problem.

Lincoln

On Wed, May 27, 2009 at 4:15 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

  we have tested three different scenarios (A, B, C) for which you can see their corresponding error logs:

(A)

* Karyotype.pm file = original version used (warnings added as you had suggested)
* 15 regions should be shown
* result: it works (i.e. it shows correctly the images, table, etc.)
* the log is:

[Wed May 27 09:50:41 2009] [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),
[Wed May 27 09:50:41 2009] [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
[Wed May 27 09:50:41 2009] [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 124.,

(B)

* Karyotype.pm file = original version used (warnings added as you had suggested)
* 800 regions should be shown
* result: it does not work
* the log is:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 212 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,
 [error]  drew image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 124.,
 [error]  about to draw image at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 122.,


(C)

* Karyotype.pm file = original version used (warnings added as you had suggested AND SUPPRESS_SMALL_CHROMOSOMES => 50000000;)
* 800 regions should be shown (same as in case B)
* result: it partially works: table is propertly shown but images (karyotype display) is off (as expected).
* the log is:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,

 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 212 (#1),

 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,
 [error]      ,

 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 208.,
 [error]  Use of uninitialized value $html in concatenation (.) or string at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 143 (#2),
 [error]      (W uninitialized) An undefined value was used as if it were already,
 [error]      defined.  It was interpreted as a "" or a 0, but maybe it was a mistake.,
 [error]      To suppress this warning assign a defined value to your variables.,
 [error]      ,
 [error]      To help you figure out what was undefined, perl will try to tell you the,
 [error]      name of the variable (if any) that was undefined. In some cases it cannot,
 [error]      do this, so it also tells you what operation you used the undefined value,
 [error]      in.  Note, however, that perl optimizes your program and the operation,
 [error]      displayed in the warning may not necessarily appear literally in your,
 [error]      program.  For example, "that $foo" is usually optimized into "that ",
 [error]      . $foo, and the warning will refer to the concatenation (.) operator,,
 [error]      even though there is no . in your program.,

cheers,
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

To turn off the karyotype display temporarily so that you can get a text table of the results, please find Bio/Graphics/Karyotype.pm and edit the following line to give it a very large value:

 use constant SUPPRESS_SMALL_CHROMOSOMES => 50;

change to

use constant SUPPRESS_SMALL_CHROMOSOMES => 50000000;

while you're at it, find line 122, which reads

my $url    = $source->generate_image($panel->gd);

and put warnings above and below it like so:

warn "about to draw image";
my $url    = $source->generate_image($panel->gd);
warn "drew image";

This will tell me whether the crash is actually occurring where I think it is.

Lincoln

On Tue, May 26, 2009 at 3:09 PM, Lincoln Stein <lincoln.stein@...> wrote:

Any luck when you change the height or width of the chromosomes?

Lincoln

On Tue, May 26, 2009 at 3:07 PM, Erick Antezana <erick.antezana@...> wrote:

Hi,

yes, the karyotype display is not working with the yeast sample data source.

Erick

---------- Forwarded message ----------
From: Lincoln Stein <lincoln.stein@...>
Date: 2009/5/26
Subject: Re: [Gmod-gbrowse] no regions are shown :-(
To: Erick Antezana <erick.antezana@...>
Cc: "gmod-gbrowse@..." <gmod-gbrowse@...>


Hi Erick,

The karyotype display is not working with the yeast sample data source either, right?

I may have to provide a way to disable the karyotype display until I can get to the bottom of this.

Lincoln

On Tue, May 26, 2009 at 11:57 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

that feature comes from a DB with about 1300 sequences (BACs). Here you are an excerpt of the GFF3 file:

##gff-version 3
#DATE: 11-27-2008_15:24:52
#Sequence       Source  Feature Start   End     Score   Strand  Phase   Attributes
3635_AAA12620   TEST   sequence        1       10680   .       +       .       ID=3635_AAA12620;Note=BAC sequence containing apex gene
3635_AAA12620   Unigene match_set       404     700     3.2E-32 +       .       ID=3633R_pc3837_c1_081870
3635_AAA12620   Unigene match_part      404     700     3.2E-32 +       .       Parent=3633R_pc3837_c1_081870

if I search over the Yeast sample data source (Yeast chromosomes 1+2), I only get:

 n1=chrI, n2=chrII at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.

I do not get the other errors (numeric comparison, etc) as with the BACs

cheers,
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

This is unexpected. I was expecting a small number of chromosome names. What type of feature is 3635_AAA12621?

Lincoln

On Tue, May 26, 2009 at 11:17 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

Here is the new excerpt (after adding the warnings):

[error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),

 [error]  n1=3635_AAA12622, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,

 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 210 (#1),
 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,

 [error]      ,
 [error]  n1=3635_AAA12621, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12623 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12621, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12620, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12628 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12628, n2=3635_AAA12629 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12622, n2=3635_AAA12627 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12625 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12621 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12626 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12620 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,
 [error]  n1=3635_AAA12627, n2=3635_AAA12624 at /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 206.,

cheers,

Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

This error may indicate some problem unrelated to libgd. Could you do me a favor and insert the following diagnostic message into line 206 of Karyotype.pm (easiest to do it directly in /usr/local/lib/perl5/site_perl...), and then send me the error log output?

 warn "n1=$n1, n2=$n2";

Thanks,

Lincoln

On Tue, May 26, 2009 at 10:47 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

I have just installed libgd 2.0.36RC1 and the problem is still there (I checked that I do not need to recompile GD; thanks for the ldd tip!).

here is an excerpt of my apache error log file:

 [error]  which: no inkscape in (/tools/bioinfo/bioim_bin:/usr/java/default/bin:/usr/local/ant/bin:/usr/bin:/bin:/usr/lib/oracle/11.1.0.1/client64/bin:/tools/bioinfo/bin:/tools/bioinfo/app/blast2/bin:/tools/bioinfo/app/Emboss/bin:/tools/bioinfo/app/psort/:/tools/bioinfo/app/tssp:/tools/bioinfo/app/t_coffee/plugins/linux),
 [error]  Argument "" isn't numeric in numeric comparison (<=>) at,
 [error]  \t/usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux/Bio/Graphics/Karyotype.pm line 210 (#1),
 [error]      (W numeric) The indicated string was fed as an argument to an operator,
 [error]      that expected a numeric value instead.  If you're fortunate the message,
 [error]      will identify which operator was so unfortunate.,

thanks again,

Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

You said:

the problem is still there although now the apache error log is more informative

What do you see in the error log?

Perhaps this isn't the libgd bug at all but something different. That would be a relief to me.

inkscape doesn't use libgd, so you don't have to worry about that. You only need to recompile GD if it is linked to libgd dynamically. The way to do this is to find GD.so, and then:

% ldd /usr/lib/perl5/auto/GD/GD.so
    linux-gate.so.1 =>  (0xb809b000)
    libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0xb802e000)
    libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb7fb7000)
    libpng12.so.0 => /usr/lib/libpng12.so.0 (0xb7f90000)
    libz.so.1 => /lib/libz.so.1 (0xb7f7a000)
    libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7f54000)
    libgd.so.2 => /usr/lib/libgd.so.2 (0xb7f13000)
    libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7db0000)
    /lib/ld-linux.so.2 (0xb809c000)

This shows that my version of GD is dynamically linked and doesn't need to be recompiled.

Lincoln

On Tue, May 26, 2009 at 10:14 AM, Erick Antezana <erick.antezana@...> wrote:

Lincoln,

 I forgot to mention that I am not getting the "child process terminated" in my error log...

 on the other hand, do I need to recompile any other package apart from GD? perhaps inkscape?

thanks
Erick

2009/5/26 Lincoln Stein <lincoln.stein@...>

Hi Erick,

Are you getting the "child process terminated" error in your apache log?

I am using GD version 2.39 without getting crashes, but the GD version is not related to the crash, as it occurs deep in libgd. However, after installing the new libgd, you may need to recompile GD.

Also, try adjusting the appearance of the karyotype:

 [builtin:karyotype]
 chrom_width  =  20
 chrom_height = 150

and variants of the above.

I had thought this problem was fixed, but apparently I need to do some more work.

Lincoln

On Tue, May 26, 2009 at 9:25 AM, Erick Antezana <erick.antezana@...> wrote:

Hi Lincoln,

 Our system had 2.0.33, we have just installed the lastest release (2.0.35) but the problem is still there although now the apache error log is more informative.... I have checked on the libgd site (http://www.libgd.org/Downloads) that the latest release is 2.0.35 but there is also a candidate release (2.0.36RC1) as well as a develompent one (2.1.0.-dev).  which version of GD would you recommend to use? (I have Bio::Graphics version 1.94)

thanks,
Erick

2009/5/25 Lincoln Stein <lincoln.stein@...>

Hi Erick,

There is a persistent bug in libgd that the karyotype display (used to show multiple hits; see enclosed) somehow triggers. Usually you will see a "child process unexpectedly terminated" in one of your apache logs -- if you are using virtual hosts, then it will be in the main error log, and not in the virutal host one.

Here are steps to try to fix the problem:

1. Install the latest Bio::Graphics from CPAN. It contains code that works around the problem.
2. Recompile libgd from the latest source.
3. Complain to me if you try (1) and (2) and the problem persists.

Lincoln

On Mon, May 25, 2009 at 11:21 AM, Erick Antezana <erick.antezana@...> wrote:

Hi,

  Our local installation of GBrowse 2.0 was successfully installed some days ago and we were testing the "Search" capabilities on specific regions and landmarks. If we look for a particular region, GBrowse is able to find it and show it. However, we got some problems to find a landmark (free text): if we use for instance the sample data source "Yeast chromosomes 1+2 (basic)" and we look for "membrane trafficking", the server shows on the top:

Yeast chromosomes 1+2 (basic): The following 66 regions match your request.

However, no region is shown below. I have checked on the Apache error log file, and there is no message. We have also tried the "Search" functionality out with our internal data and the behaviour is identical. Any suggestions?

cheers,
Erick

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://www.creativitycat.com
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse