Discussion:
[Gmod-gbrowse] Blank Page Error
Emilio A. Alvarado Ortiz
2015-10-28 23:27:38 UTC
Permalink
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:***@hci.utah.edu]
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
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 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.
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%7C22
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-----
Sent: Tuesday, October 20, 2015 10:18 AM
To: Emilio A. Alvarado Ortiz
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
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
----------------------------------------------------------------------
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<bpsl.log-1>
<bpsl.log2><Gbrowse_NotFound_Error.png>
Domain Admin
2015-10-29 12:13:15 UTC
Permalink
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
Post by 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.
[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-----
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
Post by 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 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.
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%7C22
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-----
Sent: Tuesday, October 20, 2015 10:18 AM
To: Emilio A. Alvarado Ortiz
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
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
----------------------------------------------------------------------
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Emilio A. Alvarado Ortiz
2015-10-29 20:27:34 UTC
Permalink
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]
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
Post by 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.
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 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
Post by 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 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.
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-----
Sent: Tuesday, October 20, 2015 10:18 AM
To: Emilio A. Alvarado Ortiz
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
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
----------------------------------------------------------------------
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Scott Cain
2015-10-29 22:46:41 UTC
Permalink
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 <
Post by 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 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 <
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 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 <
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-----
Sent: Tuesday, October 20, 2015 10:18 AM
To: Emilio A. Alvarado Ortiz
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 <
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
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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
Emilio A. Alvarado Ortiz
2015-10-30 22:20:48 UTC
Permalink
Hi Scott,

Thank you for your help. GBrowse is now running fine.


Regards,

-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
Post by 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.
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 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
Post by 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 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.
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 isn’t 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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