[Gmod-gbrowse] 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

[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

Post by 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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