GBrowse ( bp_seqfeature_load.pl ) Error

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GBrowse ( bp_seqfeature_load.pl ) Error

Hyunmin Kim
Hi, all

I tried to upload gff into mysql database with bp_seqfeature_load.pl

I downloaded latest GBrowse version on Github.

I tried to search this problem on google. but I can’t find the solving method.



$ bp_seqfeature_load.pl -u **** -p ***** -c -f -d human chr2_ens_annots.gff chr2.fa 2>&1 | tee /tmp/bpsl.log1

===============================================================================================
START


...
...
...
. (not full list..)
12000 features loaded in  5.19s ( 0.45s/1000 features)...
13000 features loaded in  5.63s ( 0.45s/1000 features)...
14000 features loaded in  6.08s ( 0.45s/1000 features)...
15000 features loaded in  6.53s ( 0.45s/1000 features)...
16000 features loaded in  6.98s ( 0.45s/1000 features)...
17000 features loaded in  7.42s ( 0.45s/1000 features)...
Building object tree... 0.25s4s
Loading bulk data into database... 2.55s
load time: 10.65s
loading chr2.fa...
DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1501, <GEN5> line 1165401.

-------------------- EXCEPTION --------------------
MSG: MySQL server has gone away
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_insert_sequence /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/DBI/mysql.pm:1501
STACK Bio::DB::SeqFeature::Store::insert_sequence /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store.pm:1243
STACK Bio::DB::SeqFeature::Store::Loader::load_sequence /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:619
STACK Bio::DB::SeqFeature::Store::GFF3Loader::load_line /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm:396
STACK Bio::DB::SeqFeature::Store::Loader::do_load /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:433
STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:353
STACK Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:243
STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:261
—————————————————————


END
===============================================================================================

Thanks,
Hyunmin

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Re: GBrowse ( bp_seqfeature_load.pl ) Error

Scott Cain
Hi Hyunmin,

This isn't exactly a GBrowse problem, or even necessarily a BioPerl problem (which is where the bp_seqfeature_load.pl script comes from); MySQL is shutting down for some reason (the loading script doesn't have the ability to make it shut down directly).  Please take a look in your MySQL error logs to see if there is anything there that might indicate what the problem is. 

Scott



On Fri, Apr 18, 2014 at 4:42 AM, Hyunmin Kim <[hidden email]> wrote:
Hi, all

I tried to upload gff into mysql database with bp_seqfeature_load.pl

I downloaded latest GBrowse version on Github.

I tried to search this problem on google. but I can’t find the solving method.



$ bp_seqfeature_load.pl -u **** -p ***** -c -f -d human chr2_ens_annots.gff chr2.fa 2>&1 | tee /tmp/bpsl.log1

===============================================================================================
START


...
...
...
. (not full list..)
12000 features loaded in  5.19s ( 0.45s/1000 features)...
13000 features loaded in  5.63s ( 0.45s/1000 features)...
14000 features loaded in  6.08s ( 0.45s/1000 features)...
15000 features loaded in  6.53s ( 0.45s/1000 features)...
16000 features loaded in  6.98s ( 0.45s/1000 features)...
17000 features loaded in  7.42s ( 0.45s/1000 features)...
Building object tree... 0.25s4s
Loading bulk data into database... 2.55s
load time: 10.65s
loading chr2.fa...
DBD::mysql::st execute failed: MySQL server has gone away at /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1501, <GEN5> line 1165401.

-------------------- EXCEPTION --------------------
MSG: MySQL server has gone away
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_insert_sequence /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/DBI/mysql.pm:1501
STACK Bio::DB::SeqFeature::Store::insert_sequence /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store.pm:1243
STACK Bio::DB::SeqFeature::Store::Loader::load_sequence /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:619
STACK Bio::DB::SeqFeature::Store::GFF3Loader::load_line /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/GFF3Loader.pm:396
STACK Bio::DB::SeqFeature::Store::Loader::do_load /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:433
STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:353
STACK Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl/5.14.2/Bio/DB/SeqFeature/Store/Loader.pm:243
STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:261
—————————————————————


END
===============================================================================================

Thanks,
Hyunmin

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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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

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse