[Gmod-gbrowse] Internal Server Error

Emilio A. Alvarado Ortiz

2015-12-16 20:56:20 UTC

Hello,

Hope all is well. I was modifying the âgerjam.confâ 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 âInternal Server Errorâ 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:***@scottcain.net]
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 <***@cpp.edu<mailto:***@cpp.edu>> 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:***@scottcain.net<mailto:***@scottcain.net>]
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

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.
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/
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/
stderr: DBD::SQLite::db selectcol_, referer: http://localhost/ [Wed
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-----
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 donât 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

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-----
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 itâs also possible your GFF3 is so large that youâre just running into the predefined limits of the SeqFeature store tables; these could be changed in the perl code if need be.
I donât 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 âlargeâ system in /etc/my.cnf on my system. Thatâs mostly just caches and buffer sizes, though.
Hi Timothy,
Thank you for the quick reply. When I turn off fast loading in the bp_seqfeature_load.pl<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://mysql.pm> line 1358, <GEN1> line 385675.
Thank you,
-Emilio
-----Original Message-----
Sent: Tuesday, October 20, 2015 10:18 AM
To: Emilio A. Alvarado Ortiz
ge.net<http://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<http://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 isnât so bad, sqlite is horrible with really big files).
Sometimes, sorting the GFF3 by genomic coordinates might also help.
Good luck,
Tim
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<http://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<http://bp_seqfeature_load.pl:252>
---------------------------------------------------
Thank you,
-Emilio
----------------------------------------------------------------------
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https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
<bpsl.log-1>
<bpsl.log2><Gbrowse_NotFound_Error.png>

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

Scott Cain

2015-12-16 21:37:15 UTC

Permalink

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 <

Post by Emilio A. Alvarado Ortiz
Hello,
Hope all is well. I was modifying the âgerjam.confâ 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
STACK: /usr/lib/cgi-bin/gb2/gbrowse:35
-----------------------------------------------------------
[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 âInternal
Server Errorâ 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
*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 <
Hi Scott,
I have attached the configure files that I was working on. Thank you for your help.
Regards,
-Emilio
-----Original Message-----
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 <
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
stderr: DBD::SQLite::db selectcol_ [Wed Oct 28 19:00:25 2015] [warn]

syntax error at
/opt/gbrowse/lib/perl/5.14.2/Bio/Graphics/Browser2/UserTracks/Database.pm
line 192.
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.
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/
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/
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/

stderr: DBD::SQLite::db selectcol_, referer: http://localhost/ [Wed

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/
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/
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/
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/

stderr: DBD::SQLite::db selectcol_, referer: http://localhost/ [Wed
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-----
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 donât 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 <
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-----
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 itâs also possible your GFF3 is
so large that youâre just running into the predefined limits of the
SeqFeature store tables; these could be changed in the perl code if need be.

I donât 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
âlargeâ system in /etc/my.cnf on my system. Thatâs mostly just caches and
buffer sizes, though.

On Oct 20, 2015, at 12:10 PM, Emilio A. Alvarado Ortiz <
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.