Re: Internal Server Error

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Re: Internal Server Error

eaalvarado

Hello,

 

Hope all is well. I was modifying the ‘gerjam.conf’ to add and change some tracks but the link broke. It was working fine before I started adding/deleting tracks. I checked the server error log and it says the following:

 

[Wed Dec 16 15:49:08 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: STACK: /usr/lib/cgi-bin/gb2/gbrowse:35

[Wed Dec 16 15:49:08 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: -----------------------------------------------------------

[Wed Dec 16 15:49:08 2015] [error] [client 127.0.0.1] Premature end of script headers: gbrowse

[Wed Dec 16 15:49:16 2015] [warn] mod_fcgid: cleanup zombie process 7822

 

 

When I try to access the Gerbera jamesonii browser I get an “Internal Server Error” message. I have attached the GBrowse and gerjam configuration file. Do you know a workaround this error? I would really appreciate your help.

 

 

Thank you,

 

-Emilio

 

From: Scott Cain [mailto:[hidden email]]
Sent: Thursday, October 29, 2015 3:47 PM
To: Emilio A. Alvarado Ortiz
Cc: Timothy Parnell; Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] Blank Page Error

 

Hi Emilio,

 

If you look in the GBrowse.conf file for the line that starts

 

 smtp_gateway         = localhost

 

you will notice that there is a blank space before the smtp part.  Remove that space.  Having the space there is telling it to add it on to the item before it (which reads "public_files = 10"), which is why the error message is complaining that "10 smtp_gateway..." isn't a number).

 

Scott

 

 

On Thu, Oct 29, 2015 at 4:27 PM, Emilio A. Alvarado Ortiz <[hidden email]> wrote:

Hi Scott,

I have attached the configure files that I was working on. Thank you for your help.


Regards,

-Emilio

-----Original Message-----
From: Domain Admin [mailto:[hidden email]]
Sent: Thursday, October 29, 2015 5:13 AM
To: Emilio A. Alvarado Ortiz

Cc: Timothy Parnell; Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] Blank Page Error

Hi Emilio,

I suspect you have a stray space at the beginning of a line in your configure file. Look in the file around where the smtp line is. The reason this is likely the problem is that spaces at the beginning of a line in the config indicate a continuation, so that it's concatenated to the line before it. If that doesn't make sense, or you can't find the problem, you can attach your config to your response and we can take a look.

Scott


Sent from my iPhone

> On Oct 28, 2015, at 7:27 PM, Emilio A. Alvarado Ortiz <[hidden email]> wrote:
>
> Hi Timothy,
>
> Thank you for your help on uploading the GFF and Fasta files into GBrowse. I was able to successfully upload and view everything. However, today I have been having an issue in which accessing the yeast or any other database result in a blank page. It only happens when I search for a specific database "http://localhost/fgb2/gbrowse/yeast_advanced/". I have attached a screenshot of the blank page I receive.
>
> After reading the tutorial, I checked the /var/log/apache2/error.log file and it contains the following error log:
>
> [Wed Oct 28 19:00:25 2015] [warn] [client 127.0.0.1] mod_fcgid:
> stderr: DBD::SQLite::db selectcol_ [Wed Oct 28 19:00:25 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: arrayref failed: near "smtp_gateway": syntax error at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 192.
> [Wed Oct 28 19:00:25 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Can't use an undefined value as an ARRAY reference at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 193.
> [Wed Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in numeric lt (<) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1186., referer: http://localhost/
> [Wed Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in numeric lt (<) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1193., referer: http://localhost/
> [Wed Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in subtraction (-) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1194., referer: http://localhost/
> [Wed Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid:
> stderr: DBD::SQLite::db selectcol_, referer: http://localhost/ [Wed
> Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: arrayref failed: near "smtp_gateway": syntax error at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 192., referer: http://localhost/ [Wed Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Can't use an undefined value as an ARRAY reference at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 193., referer: http://localhost/
> [Wed Oct 28 19:18:43 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in numeric lt (<) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1186., referer: http://localhost/
> [Wed Oct 28 19:18:43 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in numeric lt (<) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1193., referer: http://localhost/
> [Wed Oct 28 19:18:43 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in subtraction (-) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1194., referer: http://localhost/
> [Wed Oct 28 19:18:43 2015] [warn] [client 127.0.0.1] mod_fcgid:
> stderr: DBD::SQLite::db selectcol_, referer: http://localhost/ [Wed
> Oct 28 19:18:43 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr:
> arrayref failed: near "smtp_gateway": syntax error at
> /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database
> .pm line 192., referer: http://localhost/ [Wed Oct 28 19:18:43 2015]
> [warn] [client 127.0.0.1] mod_fcgid: stderr: Can't use an undefined
> value as an ARRAY reference at
> /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database
> .pm line 193., referer: http://localhost/
>
>
> I believe I am getting a blank page because of the "smtp_gateway" sytax error. Do you know a workaround this problem?
>
> Once again, thank you for your help.
>
>
> Regards,
>
> -Emilio
>
> -----Original Message-----
> From: Timothy Parnell [mailto:[hidden email]]
> Sent: Wednesday, October 21, 2015 9:43 PM
> To: Emilio A. Alvarado Ortiz
> Cc: Gbrowse (E-mail)
> Subject: Re: [Gmod-gbrowse] Gbrowse bp_seqfeature_load WARNING Error
>
> Hi Emilio,
> You should be able to look back at archived messages on this mailing list to find some advice; this comes up a lot. The most likely culprit is that you don’t have the chromosomes (or scaffold or reference sequence) entered in your GFF3 file. Something like
> chr1    UCSC    chromosome      1       249250621       .       .       .       Name=chr1;ID=chr1
>
> Tim
>
>> On Oct 20, 2015, at 6:55 PM, Emilio A. Alvarado Ortiz <[hidden email]> wrote:
>>
>> Hi Timothy,
>>
>> I was finally able to upload the fasta and GFF3 file using bp_seqfeature_load. I am using the GBrowse 2.52, VirtualBox Edition (32bit)  downloaded from http://gmod.org/wiki/GBrowse2_VMs. I believe the problem was the because I was running out of the /boot disk space. I increased the space by adding a new hard drive to the VM and the files successfully uploaded (see attached log).  However, now I have another issue, when I try to visualize what I just uploaded, I get a " Not Found" error. I have attached a screenshot of the error message. Do you know why it is not able to find it? I really appreciate your help.
>>
>>
>> Thank you,
>>
>> -Emilio
>>
>> -----Original Message-----
>> From: Timothy Parnell [mailto:[hidden email]]
>> Sent: Tuesday, October 20, 2015 12:21 PM
>> To: Emilio A. Alvarado Ortiz
>> Cc: Gbrowse (E-mail)
>> Subject: Re: [Gmod-gbrowse] Gbrowse bp_seqfeature_load WARNING Error
>>
>> Wow, that appears to be a really low level error that is below that of the BioPerl database adaptor. Are you running out of disk space or allocation issues where the mysql files are kept? You should solve any issues with the mysql server before dealing with the perl side of things.
>>
>> Also, make sure you use -c or create option in bp_seqfeature_load when re-loading a database; this will empty the existing tables before loading. I could imagine you might hit table limits if you keep loading and loading and loading on top of each other. I suppose it’s also possible your GFF3 is so large that you’re just running into the predefined limits of the SeqFeature store tables; these could be changed in the perl code if need be.
>>
>> I don’t know if this will help, but you may also want to consider increasing the parameters for the mysql server; I use the settings for a “large” system in /etc/my.cnf on my system. That’s mostly just caches and buffer sizes, though.
>>
>>
>> On Oct 20, 2015, at 12:10 PM, Emilio A. Alvarado Ortiz <[hidden email]<mailto:[hidden email]>> wrote:
>>
>> Hi Timothy,
>>
>> Thank you for the quick reply. When I turn off fast loading in the bp_seqfeature_load.pl load program, everything starts loading fine and then I get the same warning along with "The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358. Do you know what is triggering this error? I have attached the log file.
>>
>> --------------------- WARNING ---------------------
>> MSG: ID=666531 has been used more than once, but it cannot be found in the database.
>> This can happen if you have specified fast loading, but features sharing the same ID are not contiguous in the GFF file. This will be loaded as a separate feature.
>> Line 385661: "Lsat_1_v4_lg_1 protein2genome match_part 120131127
>> 120131795 486 - .
>> Name=gi%7C225435580%7Cref%7CXP_002283196.1%7C;ID=666531;Target=gi%7C2
>> 2
>> 5435580%7Cref%7CXP_002283196.1%7C%20200%20427;Gap=M68%20I1%20M11%20I4
>> %
>> 20M27%20I1%20M40%20D1%20M76;Scaffold=Lsat_1_v4_g_1_1079
>> "
>>
>> STACK Bio::DB::SeqFeature::Store::GFF3Loader::handle_feature
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:592
>> STACK Bio::DB::SeqFeature::Store::GFF3Loader::load_line
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:415
>> STACK Bio::DB::SeqFeature::Store::Loader::do_load
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:433
>> STACK Bio::DB::SeqFeature::Store::Loader::load_fh
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:353
>> STACK Bio::DB::SeqFeature::Store::Loader::load
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243
>> STACK toplevel /opt/gbrowse/bin/bp_seqfeature_load.pl:252
>> ---------------------------------------------------
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385661.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385661.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385662.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385662.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385663.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385663.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385664.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385664.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385665.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385665.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385666.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385666.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385667.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385667.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385668.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385668.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385669.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385669.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385670.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385670.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385671.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385671.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385672.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385672.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385673.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385673.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385674.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385674.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385675.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385675.
>>
>>
>> Thank you,
>>
>> -Emilio
>>
>> -----Original Message-----
>> From: Timothy Parnell [mailto:[hidden email]]
>> Sent: Tuesday, October 20, 2015 10:18 AM
>> To: Emilio A. Alvarado Ortiz
>> Cc:
>> [hidden email]<mailto:[hidden email]
>> ge.net>
>> Subject: Re: [Gmod-gbrowse] Gbrowse bp_seqfeature_load WARNING Error
>>
>> Hi Emilio,
>> As the error explains, your GFF3 file is re-using ID numbers. Normally, these should be unique within the file, and are used to help establish parent-child relationships. When loading, parents ideally should come before children in the GFF3 file so that they can be properly associated. When a child comes before the parent, I think it makes a dummy parent with that ID, and then throws this error when it finally comes across the parent later in the file.
>>
>> You can try turning off fast loading in the bp_seqfeature_load.pl load program, in which case out-of-order parents and children should be handled smartly. Just be prepared to let it run much, much longer (mysql isn’t so bad, sqlite is horrible with really big files).
>>
>> Sometimes, sorting the GFF3 by genomic coordinates might also help.
>>
>> Good luck,
>> Tim
>>
>> On Oct 19, 2015, at 5:23 PM, Emilio A. Alvarado Ortiz <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:
>>
>> Hello,
>>
>> I am following the GBrowse NGS Tutorial from http://gmod.org/wiki/GBrowse_NGS_Tutorial#Start but I am getting the following error when running bp_seqfeature_load.pl. I can send you the fasta and gff3 file that I am trying to upload into GBrowse. Do you know a workaround this issue? I would really appreciate your help.
>>
>>
>> loading Lsat_1_v4_lg_1_1..252823024.gff3...
>>
>> --------------------- WARNING ---------------------
>> MSG: ID=3667958 has been used more than once, but it cannot be found in the database.
>> This can happen if you have specified fast loading, but features sharing the same ID are not contiguous in the GFF file. This will be loaded as a separate feature.
>> Line 31: "Lsat_1_v4_lg_1              GeneWise_St    CDS        12608    12931    .               .               0            ID=3667958;Scaffold=Lsat_1_v4_g_1_3464
>> "
>>
>> STACK Bio::DB::SeqFeature::Store::GFF3Loader::handle_feature
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:592
>> STACK Bio::DB::SeqFeature::Store::GFF3Loader::load_line
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:415
>> STACK Bio::DB::SeqFeature::Store::Loader::do_load
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:433
>> STACK Bio::DB::SeqFeature::Store::Loader::load_fh
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:353
>> STACK Bio::DB::SeqFeature::Store::Loader::load
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243
>> STACK toplevel /opt/gbrowse/bin/bp_seqfeature_load.pl:252
>> ---------------------------------------------------
>>
>>
>> Thank you,
>>
>> -Emilio
>> ----------------------------------------------------------------------
>> -------- _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]<mailto:[hidden email]
>> ge.net><mailto:[hidden email]>
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>> <bpsl.log-1>
>>
>> <bpsl.log2><Gbrowse_NotFound_Error.png>
>
> <gbrowse_blankpage.png>
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



 

--

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


------------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

GBrowse.conf (12K) Download Attachment
gerjam.conf (6K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: Internal Server Error

Scott Cain
Hi Emilio,

While it is usually pretty difficult for me to look at a GBrowse config file and know what the problem is, we got lucky this time.  In the EST track you have a bgcolor callback, but the closing curly brace is in the first column of the line it is on, so you have the opposite problem of what you had before: you need that curly brace to be included with the lines that came before it, but because it's in the first column, the config parser thinks it is a new command.  Add one or more spaces before the brace and the problem should go away.

Here's some free, unsolicited advice for building GBrowse configs: start simple, make sure it works, and add things slowly, making sure that each new addition works as well.  If you'd have done that in this case, you would have known that the bgcolor callback was causing the problem, even if you wouldn't have realized what the problem was.  When you do that, you can send to the mailing list a question that is much more focused and likely to get a response.

Scott


On Wed, Dec 16, 2015 at 3:56 PM, Emilio A. Alvarado Ortiz <[hidden email]> wrote:

Hello,

 

Hope all is well. I was modifying the ‘gerjam.conf’ to add and change some tracks but the link broke. It was working fine before I started adding/deleting tracks. I checked the server error log and it says the following:

 

[Wed Dec 16 15:49:08 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: STACK: /usr/lib/cgi-bin/gb2/gbrowse:35

[Wed Dec 16 15:49:08 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: -----------------------------------------------------------

[Wed Dec 16 15:49:08 2015] [error] [client 127.0.0.1] Premature end of script headers: gbrowse

[Wed Dec 16 15:49:16 2015] [warn] mod_fcgid: cleanup zombie process 7822

 

 

When I try to access the Gerbera jamesonii browser I get an “Internal Server Error” message. I have attached the GBrowse and gerjam configuration file. Do you know a workaround this error? I would really appreciate your help.

 

 

Thank you,

 

-Emilio

 

From: Scott Cain [mailto:[hidden email]]
Sent: Thursday, October 29, 2015 3:47 PM
To: Emilio A. Alvarado Ortiz
Cc: Timothy Parnell; Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] Blank Page Error

 

Hi Emilio,

 

If you look in the GBrowse.conf file for the line that starts

 

 smtp_gateway         = localhost

 

you will notice that there is a blank space before the smtp part.  Remove that space.  Having the space there is telling it to add it on to the item before it (which reads "public_files = 10"), which is why the error message is complaining that "10 smtp_gateway..." isn't a number).

 

Scott

 

 

On Thu, Oct 29, 2015 at 4:27 PM, Emilio A. Alvarado Ortiz <[hidden email]> wrote:

Hi Scott,

I have attached the configure files that I was working on. Thank you for your help.


Regards,

-Emilio

-----Original Message-----
From: Domain Admin [mailto:[hidden email]]
Sent: Thursday, October 29, 2015 5:13 AM
To: Emilio A. Alvarado Ortiz

Cc: Timothy Parnell; Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] Blank Page Error

Hi Emilio,

I suspect you have a stray space at the beginning of a line in your configure file. Look in the file around where the smtp line is. The reason this is likely the problem is that spaces at the beginning of a line in the config indicate a continuation, so that it's concatenated to the line before it. If that doesn't make sense, or you can't find the problem, you can attach your config to your response and we can take a look.

Scott


Sent from my iPhone

> On Oct 28, 2015, at 7:27 PM, Emilio A. Alvarado Ortiz <[hidden email]> wrote:
>
> Hi Timothy,
>
> Thank you for your help on uploading the GFF and Fasta files into GBrowse. I was able to successfully upload and view everything. However, today I have been having an issue in which accessing the yeast or any other database result in a blank page. It only happens when I search for a specific database "http://localhost/fgb2/gbrowse/yeast_advanced/". I have attached a screenshot of the blank page I receive.
>
> After reading the tutorial, I checked the /var/log/apache2/error.log file and it contains the following error log:
>
> [Wed Oct 28 19:00:25 2015] [warn] [client 127.0.0.1] mod_fcgid:
> stderr: DBD::SQLite::db selectcol_ [Wed Oct 28 19:00:25 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: arrayref failed: near "smtp_gateway": syntax error at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 192.
> [Wed Oct 28 19:00:25 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Can't use an undefined value as an ARRAY reference at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 193.
> [Wed Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in numeric lt (<) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1186., referer: http://localhost/
> [Wed Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in numeric lt (<) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1193., referer: http://localhost/
> [Wed Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in subtraction (-) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1194., referer: http://localhost/
> [Wed Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid:
> stderr: DBD::SQLite::db selectcol_, referer: http://localhost/ [Wed
> Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: arrayref failed: near "smtp_gateway": syntax error at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 192., referer: http://localhost/ [Wed Oct 28 19:18:39 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Can't use an undefined value as an ARRAY reference at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm line 193., referer: http://localhost/
> [Wed Oct 28 19:18:43 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in numeric lt (<) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1186., referer: http://localhost/
> [Wed Oct 28 19:18:43 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in numeric lt (<) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1193., referer: http://localhost/
> [Wed Oct 28 19:18:43 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr: Argument "10 smtp_gateway         = localhost" isn't numeric in subtraction (-) at /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/Render/HTML.pm line 1194., referer: http://localhost/
> [Wed Oct 28 19:18:43 2015] [warn] [client 127.0.0.1] mod_fcgid:
> stderr: DBD::SQLite::db selectcol_, referer: http://localhost/ [Wed
> Oct 28 19:18:43 2015] [warn] [client 127.0.0.1] mod_fcgid: stderr:
> arrayref failed: near "smtp_gateway": syntax error at
> /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database
> .pm line 192., referer: http://localhost/ [Wed Oct 28 19:18:43 2015]
> [warn] [client 127.0.0.1] mod_fcgid: stderr: Can't use an undefined
> value as an ARRAY reference at
> /opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database
> .pm line 193., referer: http://localhost/
>
>
> I believe I am getting a blank page because of the "smtp_gateway" sytax error. Do you know a workaround this problem?
>
> Once again, thank you for your help.
>
>
> Regards,
>
> -Emilio
>
> -----Original Message-----
> From: Timothy Parnell [mailto:[hidden email]]
> Sent: Wednesday, October 21, 2015 9:43 PM
> To: Emilio A. Alvarado Ortiz
> Cc: Gbrowse (E-mail)
> Subject: Re: [Gmod-gbrowse] Gbrowse bp_seqfeature_load WARNING Error
>
> Hi Emilio,
> You should be able to look back at archived messages on this mailing list to find some advice; this comes up a lot. The most likely culprit is that you don’t have the chromosomes (or scaffold or reference sequence) entered in your GFF3 file. Something like
> chr1    UCSC    chromosome      1       249250621       .       .       .       Name=chr1;ID=chr1
>
> Tim
>
>> On Oct 20, 2015, at 6:55 PM, Emilio A. Alvarado Ortiz <[hidden email]> wrote:
>>
>> Hi Timothy,
>>
>> I was finally able to upload the fasta and GFF3 file using bp_seqfeature_load. I am using the GBrowse 2.52, VirtualBox Edition (32bit)  downloaded from http://gmod.org/wiki/GBrowse2_VMs. I believe the problem was the because I was running out of the /boot disk space. I increased the space by adding a new hard drive to the VM and the files successfully uploaded (see attached log).  However, now I have another issue, when I try to visualize what I just uploaded, I get a " Not Found" error. I have attached a screenshot of the error message. Do you know why it is not able to find it? I really appreciate your help.
>>
>>
>> Thank you,
>>
>> -Emilio
>>
>> -----Original Message-----
>> From: Timothy Parnell [mailto:[hidden email]]
>> Sent: Tuesday, October 20, 2015 12:21 PM
>> To: Emilio A. Alvarado Ortiz
>> Cc: Gbrowse (E-mail)
>> Subject: Re: [Gmod-gbrowse] Gbrowse bp_seqfeature_load WARNING Error
>>
>> Wow, that appears to be a really low level error that is below that of the BioPerl database adaptor. Are you running out of disk space or allocation issues where the mysql files are kept? You should solve any issues with the mysql server before dealing with the perl side of things.
>>
>> Also, make sure you use -c or create option in bp_seqfeature_load when re-loading a database; this will empty the existing tables before loading. I could imagine you might hit table limits if you keep loading and loading and loading on top of each other. I suppose it’s also possible your GFF3 is so large that you’re just running into the predefined limits of the SeqFeature store tables; these could be changed in the perl code if need be.
>>
>> I don’t know if this will help, but you may also want to consider increasing the parameters for the mysql server; I use the settings for a “large” system in /etc/my.cnf on my system. That’s mostly just caches and buffer sizes, though.
>>
>>
>> On Oct 20, 2015, at 12:10 PM, Emilio A. Alvarado Ortiz <[hidden email]<mailto:[hidden email]>> wrote:
>>
>> Hi Timothy,
>>
>> Thank you for the quick reply. When I turn off fast loading in the bp_seqfeature_load.pl load program, everything starts loading fine and then I get the same warning along with "The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358. Do you know what is triggering this error? I have attached the log file.
>>
>> --------------------- WARNING ---------------------
>> MSG: ID=666531 has been used more than once, but it cannot be found in the database.
>> This can happen if you have specified fast loading, but features sharing the same ID are not contiguous in the GFF file. This will be loaded as a separate feature.
>> Line 385661: "Lsat_1_v4_lg_1 protein2genome match_part 120131127
>> 120131795 486 - .
>> Name=gi%7C225435580%7Cref%7CXP_002283196.1%7C;ID=666531;Target=gi%7C2
>> 2
>> 5435580%7Cref%7CXP_002283196.1%7C%20200%20427;Gap=M68%20I1%20M11%20I4
>> %
>> 20M27%20I1%20M40%20D1%20M76;Scaffold=Lsat_1_v4_g_1_1079
>> "
>>
>> STACK Bio::DB::SeqFeature::Store::GFF3Loader::handle_feature
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:592
>> STACK Bio::DB::SeqFeature::Store::GFF3Loader::load_line
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:415
>> STACK Bio::DB::SeqFeature::Store::Loader::do_load
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:433
>> STACK Bio::DB::SeqFeature::Store::Loader::load_fh
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:353
>> STACK Bio::DB::SeqFeature::Store::Loader::load
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243
>> STACK toplevel /opt/gbrowse/bin/bp_seqfeature_load.pl:252
>> ---------------------------------------------------
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385661.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385661.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385662.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385662.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385663.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385663.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385664.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385664.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385665.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385665.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385666.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385666.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385667.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385667.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385668.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385668.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385669.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385669.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385670.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385670.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385671.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385671.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385672.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385672.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385673.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385673.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385674.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385674.
>> DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385675.
>> Transaction aborted because DBD::mysql::st execute failed: The table 'feature' is full at /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1358, <GEN1> line 385675.
>>
>>
>> Thank you,
>>
>> -Emilio
>>
>> -----Original Message-----
>> From: Timothy Parnell [mailto:[hidden email]]
>> Sent: Tuesday, October 20, 2015 10:18 AM
>> To: Emilio A. Alvarado Ortiz
>> Cc:
>> [hidden email]<mailto:[hidden email]
>> ge.net>
>> Subject: Re: [Gmod-gbrowse] Gbrowse bp_seqfeature_load WARNING Error
>>
>> Hi Emilio,
>> As the error explains, your GFF3 file is re-using ID numbers. Normally, these should be unique within the file, and are used to help establish parent-child relationships. When loading, parents ideally should come before children in the GFF3 file so that they can be properly associated. When a child comes before the parent, I think it makes a dummy parent with that ID, and then throws this error when it finally comes across the parent later in the file.
>>
>> You can try turning off fast loading in the bp_seqfeature_load.pl load program, in which case out-of-order parents and children should be handled smartly. Just be prepared to let it run much, much longer (mysql isn’t so bad, sqlite is horrible with really big files).
>>
>> Sometimes, sorting the GFF3 by genomic coordinates might also help.
>>
>> Good luck,
>> Tim
>>
>> On Oct 19, 2015, at 5:23 PM, Emilio A. Alvarado Ortiz <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:
>>
>> Hello,
>>
>> I am following the GBrowse NGS Tutorial from http://gmod.org/wiki/GBrowse_NGS_Tutorial#Start but I am getting the following error when running bp_seqfeature_load.pl. I can send you the fasta and gff3 file that I am trying to upload into GBrowse. Do you know a workaround this issue? I would really appreciate your help.
>>
>>
>> loading Lsat_1_v4_lg_1_1..252823024.gff3...
>>
>> --------------------- WARNING ---------------------
>> MSG: ID=3667958 has been used more than once, but it cannot be found in the database.
>> This can happen if you have specified fast loading, but features sharing the same ID are not contiguous in the GFF file. This will be loaded as a separate feature.
>> Line 31: "Lsat_1_v4_lg_1              GeneWise_St    CDS        12608    12931    .               .               0            ID=3667958;Scaffold=Lsat_1_v4_g_1_3464
>> "
>>
>> STACK Bio::DB::SeqFeature::Store::GFF3Loader::handle_feature
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:592
>> STACK Bio::DB::SeqFeature::Store::GFF3Loader::load_line
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:415
>> STACK Bio::DB::SeqFeature::Store::Loader::do_load
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:433
>> STACK Bio::DB::SeqFeature::Store::Loader::load_fh
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:353
>> STACK Bio::DB::SeqFeature::Store::Loader::load
>> /opt/gbrowse/lib/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243
>> STACK toplevel /opt/gbrowse/bin/bp_seqfeature_load.pl:252
>> ---------------------------------------------------
>>
>>
>> Thank you,
>>
>> -Emilio
>> ----------------------------------------------------------------------
>> -------- _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]<mailto:[hidden email]
>> ge.net><mailto:[hidden email]>
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>> <bpsl.log-1>
>>
>> <bpsl.log2><Gbrowse_NotFound_Error.png>
>
> <gbrowse_blankpage.png>
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




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

------------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse