From johnson.biotech at gmail.com Wed Sep 13 11:06:28 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Wed, 13 Sep 2006 11:06:28 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error Message-ID: Hello, I'm a newbie to BioSQl, trying to set it up on mySQL server following the installation directions and ran into a problem. When trying to load the taxonomic info, I get an error at 230000+ line. Progress dump follows. Have I missed anything??? ======================================= # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port 3306 -dbuser root -dbpass xxxxx -verbose=2 -download Loading NCBI taxon database in taxdata: ... retrieving all taxon nodes in the database ... reading in taxon nodes from nodes.dmp ... insert / update / delete taxon nodes 10000/324120 done (in 15 secs, 666.7 rows/s) 20000/324120 done (in 15 secs, 666.7 rows/s) 30000/324120 done (in 15 secs, 666.7 rows/s) 40000/324120 done (in 15 secs, 666.7 rows/s) 50000/324120 done (in 15 secs, 666.7 rows/s) 60000/324120 done (in 14 secs, 714.3 rows/s) 70000/324120 done (in 15 secs, 666.7 rows/s) 80000/324120 done (in 14 secs, 714.3 rows/s) 90000/324120 done (in 15 secs, 666.7 rows/s) 100000/324120 done (in 14 secs, 714.3 rows/s) 110000/324120 done (in 16 secs, 625.0 rows/s) 120000/324120 done (in 15 secs, 666.7 rows/s) 130000/324120 done (in 14 secs, 714.3 rows/s) 140000/324120 done (in 15 secs, 666.7 rows/s) 150000/324120 done (in 15 secs, 666.7 rows/s) 160000/324120 done (in 14 secs, 714.3 rows/s) 170000/324120 done (in 14 secs, 714.3 rows/s) 180000/324120 done (in 15 secs, 666.7 rows/s) 190000/324120 done (in 15 secs, 666.7 rows/s) 200000/324120 done (in 14 secs, 714.3 rows/s) 210000/324120 done (in 15 secs, 666.7 rows/s) 220000/324120 done (in 14 secs, 714.3 rows/s) 230000/324120 done (in 15 secs, 666.7 rows/s) failed to insert node (281015;281015;3817;species;1;1): Error writing file '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. # =================================================== -- Best Regards, Seth Johnson Senior Bioinformatics Associate Ph: (202) 470-0900 Fx: (775) 251-0358 From johnson.biotech at gmail.com Wed Sep 13 13:43:45 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Wed, 13 Sep 2006 13:43:45 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: References: Message-ID: That would be strange since I've tried it on Sun Solaris and Windows XP (with gigs of free space) with same exact results. On 9/13/06, aaron.j.mackey at gsk.com wrote: > > Most likely you've run out of space in /var/tmp ... > > -Aaron > > biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM: > > > Hello, > > I'm a newbie to BioSQl, trying to set it up on mySQL server following > the > > installation directions and ran into a problem. When trying to load the > > taxonomic info, I get an error at 230000+ line. Progress dump follows. > > Have I missed anything??? > > ======================================= > > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port 3306 > > -dbuser root -dbpass xxxxx -verbose=2 -download > > Loading NCBI taxon database in taxdata: > > ... retrieving all taxon nodes in the database > > ... reading in taxon nodes from nodes.dmp > > ... insert / update / delete taxon nodes > > 10000/324120 done (in 15 secs, 666.7 rows/s) > > 20000/324120 done (in 15 secs, 666.7 rows/s) > > 30000/324120 done (in 15 secs, 666.7 rows/s) > > 40000/324120 done (in 15 secs, 666.7 rows/s) > > 50000/324120 done (in 15 secs, 666.7 rows/s) > > 60000/324120 done (in 14 secs, 714.3 rows/s) > > 70000/324120 done (in 15 secs, 666.7 rows/s) > > 80000/324120 done (in 14 secs, 714.3 rows/s) > > 90000/324120 done (in 15 secs, 666.7 rows/s) > > 100000/324120 done (in 14 secs, 714.3 rows/s) > > 110000/324120 done (in 16 secs, 625.0 rows/s) > > 120000/324120 done (in 15 secs, 666.7 rows/s) > > 130000/324120 done (in 14 secs, 714.3 rows/s) > > 140000/324120 done (in 15 secs, 666.7 rows/s) > > 150000/324120 done (in 15 secs, 666.7 rows/s) > > 160000/324120 done (in 14 secs, 714.3 rows/s) > > 170000/324120 done (in 14 secs, 714.3 rows/s) > > 180000/324120 done (in 15 secs, 666.7 rows/s) > > 190000/324120 done (in 15 secs, 666.7 rows/s) > > 200000/324120 done (in 14 secs, 714.3 rows/s) > > 210000/324120 done (in 15 secs, 666.7 rows/s) > > 220000/324120 done (in 14 secs, 714.3 rows/s) > > 230000/324120 done (in 15 secs, 666.7 rows/s) > > failed to insert node (281015;281015;3817;species;1;1): Error writing > file > > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. > > # > > =================================================== > > > > > > -- > > Best Regards, > > > > > > Seth Johnson > > Senior Bioinformatics Associate > > > > Ph: (202) 470-0900 > > Fx: (775) 251-0358 > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > -- Best Regards, Seth Johnson Senior Bioinformatics Associate Ph: (202) 470-0900 Fx: (775) 251-0358 From hlapp at gmx.net Wed Sep 13 13:47:44 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Sep 2006 13:47:44 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: References: Message-ID: <47430222-BE83-495D-8CF0-98E9B2B8C98E@gmx.net> This looks like an issue with your mysql server to me. Maybe you are running out of diskspace or exceeding your quota? -hilmar On Sep 13, 2006, at 11:06 AM, Seth Johnson wrote: > Hello, > I'm a newbie to BioSQl, trying to set it up on mySQL server > following the > installation directions and ran into a problem. When trying to > load the > taxonomic info, I get an error at 230000+ line. Progress dump > follows. > Have I missed anything??? > ======================================= > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port > 3306 > -dbuser root -dbpass xxxxx -verbose=2 -download > Loading NCBI taxon database in taxdata: > ... retrieving all taxon nodes in the database > ... reading in taxon nodes from nodes.dmp > ... insert / update / delete taxon nodes > 10000/324120 done (in 15 secs, 666.7 rows/s) > 20000/324120 done (in 15 secs, 666.7 rows/s) > 30000/324120 done (in 15 secs, 666.7 rows/s) > 40000/324120 done (in 15 secs, 666.7 rows/s) > 50000/324120 done (in 15 secs, 666.7 rows/s) > 60000/324120 done (in 14 secs, 714.3 rows/s) > 70000/324120 done (in 15 secs, 666.7 rows/s) > 80000/324120 done (in 14 secs, 714.3 rows/s) > 90000/324120 done (in 15 secs, 666.7 rows/s) > 100000/324120 done (in 14 secs, 714.3 rows/s) > 110000/324120 done (in 16 secs, 625.0 rows/s) > 120000/324120 done (in 15 secs, 666.7 rows/s) > 130000/324120 done (in 14 secs, 714.3 rows/s) > 140000/324120 done (in 15 secs, 666.7 rows/s) > 150000/324120 done (in 15 secs, 666.7 rows/s) > 160000/324120 done (in 14 secs, 714.3 rows/s) > 170000/324120 done (in 14 secs, 714.3 rows/s) > 180000/324120 done (in 15 secs, 666.7 rows/s) > 190000/324120 done (in 15 secs, 666.7 rows/s) > 200000/324120 done (in 14 secs, 714.3 rows/s) > 210000/324120 done (in 15 secs, 666.7 rows/s) > 220000/324120 done (in 14 secs, 714.3 rows/s) > 230000/324120 done (in 15 secs, 666.7 rows/s) > failed to insert node (281015;281015;3817;species;1;1): Error > writing file > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. > # > =================================================== > > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > > Ph: (202) 470-0900 > Fx: (775) 251-0358 > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Wed Sep 13 14:00:29 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Sep 2006 14:00:29 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: References: Message-ID: <87000731-2991-490C-9824-7AAAAACE8F8C@gmx.net> Well I don't know about your systems but as a matter of fact it is a mysql error that is reported here, so it is clearly the mysql server which is causing the issue. When you say you've tried on different platforms, did you only run the script on different platforms or did you also install and set up and use the mysql server on the different (local) platforms? -hilmar On Sep 13, 2006, at 1:43 PM, Seth Johnson wrote: > That would be strange since I've tried it on Sun Solaris and > Windows XP > (with gigs of free space) with same exact results. > > On 9/13/06, aaron.j.mackey at gsk.com wrote: >> >> Most likely you've run out of space in /var/tmp ... >> >> -Aaron >> >> biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM: >> >>> Hello, >>> I'm a newbie to BioSQl, trying to set it up on mySQL server >>> following >> the >>> installation directions and ran into a problem. When trying to >>> load the >>> taxonomic info, I get an error at 230000+ line. Progress dump >>> follows. >>> Have I missed anything??? >>> ======================================= >>> # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost - >>> port 3306 >>> -dbuser root -dbpass xxxxx -verbose=2 -download >>> Loading NCBI taxon database in taxdata: >>> ... retrieving all taxon nodes in the database >>> ... reading in taxon nodes from nodes.dmp >>> ... insert / update / delete taxon nodes >>> 10000/324120 done (in 15 secs, 666.7 rows/s) >>> 20000/324120 done (in 15 secs, 666.7 rows/s) >>> 30000/324120 done (in 15 secs, 666.7 rows/s) >>> 40000/324120 done (in 15 secs, 666.7 rows/s) >>> 50000/324120 done (in 15 secs, 666.7 rows/s) >>> 60000/324120 done (in 14 secs, 714.3 rows/s) >>> 70000/324120 done (in 15 secs, 666.7 rows/s) >>> 80000/324120 done (in 14 secs, 714.3 rows/s) >>> 90000/324120 done (in 15 secs, 666.7 rows/s) >>> 100000/324120 done (in 14 secs, 714.3 rows/s) >>> 110000/324120 done (in 16 secs, 625.0 rows/s) >>> 120000/324120 done (in 15 secs, 666.7 rows/s) >>> 130000/324120 done (in 14 secs, 714.3 rows/s) >>> 140000/324120 done (in 15 secs, 666.7 rows/s) >>> 150000/324120 done (in 15 secs, 666.7 rows/s) >>> 160000/324120 done (in 14 secs, 714.3 rows/s) >>> 170000/324120 done (in 14 secs, 714.3 rows/s) >>> 180000/324120 done (in 15 secs, 666.7 rows/s) >>> 190000/324120 done (in 15 secs, 666.7 rows/s) >>> 200000/324120 done (in 14 secs, 714.3 rows/s) >>> 210000/324120 done (in 15 secs, 666.7 rows/s) >>> 220000/324120 done (in 14 secs, 714.3 rows/s) >>> 230000/324120 done (in 15 secs, 666.7 rows/s) >>> failed to insert node (281015;281015;3817;species;1;1): Error >>> writing >> file >>> '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. >>> # >>> =================================================== >>> >>> >>> -- >>> Best Regards, >>> >>> >>> Seth Johnson >>> Senior Bioinformatics Associate >>> >>> Ph: (202) 470-0900 >>> Fx: (775) 251-0358 >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >> >> >> > > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > > Ph: (202) 470-0900 > Fx: (775) 251-0358 > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From johnson.biotech at gmail.com Wed Sep 13 14:01:16 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Wed, 13 Sep 2006 14:01:16 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: References: Message-ID: Sorry, it didn't occur to me that running out of space was MySQL related. :) On 9/13/06, aaron.j.mackey at gsk.com wrote: > > strange or not, that is exactly what MySQL error 28 means: no space left > on device. > > -Aaron > > "Seth Johnson" wrote on 09/13/2006 01:43:45 > PM: > > > That would be strange since I've tried it on Sun Solaris and Windows > > XP (with gigs of free space) with same exact results. > > > On 9/13/06, aaron.j.mackey at gsk.com wrote: > > Most likely you've run out of space in /var/tmp ... > > > > -Aaron > > > > biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM: > > > > > Hello, > > > I'm a newbie to BioSQl, trying to set it up on mySQL server following > > the > > > installation directions and ran into a problem. When trying to load > the > > > taxonomic info, I get an error at 230000+ line. Progress dump > follows. > > > Have I missed anything??? > > > ======================================= > > > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port > 3306 > > > -dbuser root -dbpass xxxxx -verbose=2 -download > > > Loading NCBI taxon database in taxdata: > > > ... retrieving all taxon nodes in the database > > > ... reading in taxon nodes from nodes.dmp > > > ... insert / update / delete taxon nodes > > > 10000/324120 done (in 15 secs, 666.7 rows/s) > > > 20000/324120 done (in 15 secs, 666.7 rows/s) > > > 30000/324120 done (in 15 secs, 666.7 rows/s) > > > 40000/324120 done (in 15 secs, 666.7 rows/s) > > > 50000/324120 done (in 15 secs, 666.7 rows/s) > > > 60000/324120 done (in 14 secs, 714.3 rows/s) > > > 70000/324120 done (in 15 secs, 666.7 rows/s) > > > 80000/324120 done (in 14 secs, 714.3 rows/s) > > > 90000/324120 done (in 15 secs, 666.7 rows/s) > > > 100000/324120 done (in 14 secs, 714.3 rows/s) > > > 110000/324120 done (in 16 secs, 625.0 rows/s) > > > 120000/324120 done (in 15 secs, 666.7 rows/s) > > > 130000/324120 done (in 14 secs, 714.3 rows/s) > > > 140000/324120 done (in 15 secs, 666.7 rows/s) > > > 150000/324120 done (in 15 secs, 666.7 rows/s) > > > 160000/324120 done (in 14 secs, 714.3 rows/s) > > > 170000/324120 done (in 14 secs, 714.3 rows/s) > > > 180000/324120 done (in 15 secs, 666.7 rows/s) > > > 190000/324120 done (in 15 secs, 666.7 rows/s) > > > 200000/324120 done (in 14 secs, 714.3 rows/s) > > > 210000/324120 done (in 15 secs, 666.7 rows/s) > > > 220000/324120 done (in 14 secs, 714.3 rows/s) > > > 230000/324120 done (in 15 secs, 666.7 rows/s) > > > failed to insert node (281015;281015;3817;species;1;1): Error writing > > file > > > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. > > > # > > > =================================================== > > > > > > > > > -- > > > Best Regards, > > > > > > > > > Seth Johnson > > > Senior Bioinformatics Associate > > > > > > Ph: (202) 470-0900 > > > Fx: (775) 251-0358 > > > _______________________________________________ > > > BioSQL-l mailing list > > > BioSQL-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > > > > > > > > > > -- > > Best Regards, > > > > > > Seth Johnson > > Senior Bioinformatics Associate > > > > Ph: (202) 470-0900 > > Fx: (775) 251-0358 > > -- Best Regards, Seth Johnson Senior Bioinformatics Associate Ph: (202) 470-0900 Fx: (775) 251-0358 From aaron.j.mackey at gsk.com Wed Sep 13 12:27:44 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Wed, 13 Sep 2006 12:27:44 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: Message-ID: Most likely you've run out of space in /var/tmp ... -Aaron biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM: > Hello, > I'm a newbie to BioSQl, trying to set it up on mySQL server following the > installation directions and ran into a problem. When trying to load the > taxonomic info, I get an error at 230000+ line. Progress dump follows. > Have I missed anything??? > ======================================= > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port 3306 > -dbuser root -dbpass xxxxx -verbose=2 -download > Loading NCBI taxon database in taxdata: > ... retrieving all taxon nodes in the database > ... reading in taxon nodes from nodes.dmp > ... insert / update / delete taxon nodes > 10000/324120 done (in 15 secs, 666.7 rows/s) > 20000/324120 done (in 15 secs, 666.7 rows/s) > 30000/324120 done (in 15 secs, 666.7 rows/s) > 40000/324120 done (in 15 secs, 666.7 rows/s) > 50000/324120 done (in 15 secs, 666.7 rows/s) > 60000/324120 done (in 14 secs, 714.3 rows/s) > 70000/324120 done (in 15 secs, 666.7 rows/s) > 80000/324120 done (in 14 secs, 714.3 rows/s) > 90000/324120 done (in 15 secs, 666.7 rows/s) > 100000/324120 done (in 14 secs, 714.3 rows/s) > 110000/324120 done (in 16 secs, 625.0 rows/s) > 120000/324120 done (in 15 secs, 666.7 rows/s) > 130000/324120 done (in 14 secs, 714.3 rows/s) > 140000/324120 done (in 15 secs, 666.7 rows/s) > 150000/324120 done (in 15 secs, 666.7 rows/s) > 160000/324120 done (in 14 secs, 714.3 rows/s) > 170000/324120 done (in 14 secs, 714.3 rows/s) > 180000/324120 done (in 15 secs, 666.7 rows/s) > 190000/324120 done (in 15 secs, 666.7 rows/s) > 200000/324120 done (in 14 secs, 714.3 rows/s) > 210000/324120 done (in 15 secs, 666.7 rows/s) > 220000/324120 done (in 14 secs, 714.3 rows/s) > 230000/324120 done (in 15 secs, 666.7 rows/s) > failed to insert node (281015;281015;3817;species;1;1): Error writing file > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. > # > =================================================== > > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > > Ph: (202) 470-0900 > Fx: (775) 251-0358 > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > From aaron.j.mackey at gsk.com Wed Sep 13 13:49:58 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Wed, 13 Sep 2006 13:49:58 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: Message-ID: strange or not, that is exactly what MySQL error 28 means: no space left on device. -Aaron "Seth Johnson" wrote on 09/13/2006 01:43:45 PM: > That would be strange since I've tried it on Sun Solaris and Windows > XP (with gigs of free space) with same exact results. > On 9/13/06, aaron.j.mackey at gsk.com wrote: > Most likely you've run out of space in /var/tmp ... > > -Aaron > > biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM: > > > Hello, > > I'm a newbie to BioSQl, trying to set it up on mySQL server following > the > > installation directions and ran into a problem. When trying to load the > > taxonomic info, I get an error at 230000+ line. Progress dump follows. > > Have I missed anything??? > > ======================================= > > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port 3306 > > -dbuser root -dbpass xxxxx -verbose=2 -download > > Loading NCBI taxon database in taxdata: > > ... retrieving all taxon nodes in the database > > ... reading in taxon nodes from nodes.dmp > > ... insert / update / delete taxon nodes > > 10000/324120 done (in 15 secs, 666.7 rows/s) > > 20000/324120 done (in 15 secs, 666.7 rows/s) > > 30000/324120 done (in 15 secs, 666.7 rows/s) > > 40000/324120 done (in 15 secs, 666.7 rows/s) > > 50000/324120 done (in 15 secs, 666.7 rows/s) > > 60000/324120 done (in 14 secs, 714.3 rows/s) > > 70000/324120 done (in 15 secs, 666.7 rows/s) > > 80000/324120 done (in 14 secs, 714.3 rows/s) > > 90000/324120 done (in 15 secs, 666.7 rows/s) > > 100000/324120 done (in 14 secs, 714.3 rows/s) > > 110000/324120 done (in 16 secs, 625.0 rows/s) > > 120000/324120 done (in 15 secs, 666.7 rows/s) > > 130000/324120 done (in 14 secs, 714.3 rows/s) > > 140000/324120 done (in 15 secs, 666.7 rows/s) > > 150000/324120 done (in 15 secs, 666.7 rows/s) > > 160000/324120 done (in 14 secs, 714.3 rows/s) > > 170000/324120 done (in 14 secs, 714.3 rows/s) > > 180000/324120 done (in 15 secs, 666.7 rows/s) > > 190000/324120 done (in 15 secs, 666.7 rows/s) > > 200000/324120 done (in 14 secs, 714.3 rows/s) > > 210000/324120 done (in 15 secs, 666.7 rows/s) > > 220000/324120 done (in 14 secs, 714.3 rows/s) > > 230000/324120 done (in 15 secs, 666.7 rows/s) > > failed to insert node (281015;281015;3817;species;1;1): Error writing > file > > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. > > # > > =================================================== > > > > > > -- > > Best Regards, > > > > > > Seth Johnson > > Senior Bioinformatics Associate > > > > Ph: (202) 470-0900 > > Fx: (775) 251-0358 > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > > Ph: (202) 470-0900 > Fx: (775) 251-0358 From gwu at molbio.mgh.harvard.edu Tue Sep 26 21:33:38 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 26 Sep 2006 21:33:38 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: References: Message-ID: <4519D4F2.4060001@molbio.mgh.harvard.edu> Hi Everyone, I finally finished loading some Genbank genome sequences(Arabidopsis thaliana and C. elegans) into my MySQL(5.0.19 on Redhad AS 4) BioSQL database though the load_seqdatabase.pl works extremely slow(If -debug is turned on, a lot of messages about not able to find adaptor class for Bio::Annotation::TypeManager. Is this about the dynamic library loading issue mention in one of Hilmar's message?). Now I'm writing views and stored procedures so other projects can easily retrieve specific information. But so far I have not figured out how to write a SQL statement to list all genes of the genomes. Can anyone show me how to get the information or let me know where to find related document? Thanks in advance. Gang From gwu at molbio.mgh.harvard.edu Wed Sep 27 09:53:21 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Wed, 27 Sep 2006 09:53:21 -0400 Subject: [BioSQL-l] how to retrieve specific information from BioSQL database In-Reply-To: <4519D4F2.4060001@molbio.mgh.harvard.edu> References: <4519D4F2.4060001@molbio.mgh.harvard.edu> Message-ID: <451A8251.5060302@molbio.mgh.harvard.edu> Hi Everyone, I finally finished loading some Genbank genome sequences(Arabidopsis thaliana and C. elegans) into my MySQL(5.0.19 on Redhad AS 4) BioSQL database though the load_seqdatabase.pl works extremely slow(If -debug is turned on, a lot of messages about not able to find adaptor class for Bio::Annotation::TypeManager. Is this about the dynamic library loading issue mention in one of Hilmar's message?). Now I'm writing views and stored procedures so other projects can easily retrieve specific information. But so far I have not figured out how to write a SQL statement to list all genes of the genomes. Can anyone show me how to get the information or let me know where to find related document? Thanks in advance. Gang From johnson.biotech at gmail.com Wed Sep 27 13:39:05 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Wed, 27 Sep 2006 13:39:05 -0400 Subject: [BioSQL-l] Error retrieving sequence from BioSQL Message-ID: Hello guys, I successfully populated the biosql database, thanks to you. Now, I'm trying to retrieve a sequence from it following the example from BOSC2003 slides and ran into uninformative error (at least to me it doesn't mean anyting). I suspect that I'm missing something and hope you can point me in the right direction. Here's my source code: ------------------------------------------------------------------------- #!/usr/bin/perl -w use strict; use warnings; use Bio::Seq; use Bio::Seq::SeqFactory; use Bio::DB::SimpleDBContext; use Bio::DB::BioDB; my $dbc = Bio::DB::SimpleDBContext->new( -driver => 'mysql', -dbname => 'BioSQL_1', -host => '192.168.1.3', -user => 'xxxxx', -pass => 'xxxxxx' ); my $db = Bio::DB::BioDB->new(-database => 'biosql', -dbcontext => $dbc); my $seq = Bio::Seq->new(-accession_number => 'NM_014580', -namespace => 'refseq_H_sapiens'); my $seqfact = Bio::Seq::SeqFactory->new(-type => 'Bio::Seq'); my $adp = $db->get_object_adaptor($seq); my $dbseq = $adp->find_by_unique_key($seq, -obj_factory => $seqfact); my $out = Bio::SeqIO->newFh('-format' => 'EMBL'); print $out $dbseq; exit; ----------------------------------------------------------------- Just when the "find_by_unique_key" function is executed I get the following error: ================================ Undefined subroutine &Bio::Root::Root::throw called at c:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm line 199. ================================ The sequence does exist in the database. I checked that. Any ideas??? -- Best Regards, Seth Johnson Senior Bioinformatics Associate From johnson.biotech at gmail.com Wed Sep 13 15:06:28 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Wed, 13 Sep 2006 11:06:28 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error Message-ID: Hello, I'm a newbie to BioSQl, trying to set it up on mySQL server following the installation directions and ran into a problem. When trying to load the taxonomic info, I get an error at 230000+ line. Progress dump follows. Have I missed anything??? ======================================= # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port 3306 -dbuser root -dbpass xxxxx -verbose=2 -download Loading NCBI taxon database in taxdata: ... retrieving all taxon nodes in the database ... reading in taxon nodes from nodes.dmp ... insert / update / delete taxon nodes 10000/324120 done (in 15 secs, 666.7 rows/s) 20000/324120 done (in 15 secs, 666.7 rows/s) 30000/324120 done (in 15 secs, 666.7 rows/s) 40000/324120 done (in 15 secs, 666.7 rows/s) 50000/324120 done (in 15 secs, 666.7 rows/s) 60000/324120 done (in 14 secs, 714.3 rows/s) 70000/324120 done (in 15 secs, 666.7 rows/s) 80000/324120 done (in 14 secs, 714.3 rows/s) 90000/324120 done (in 15 secs, 666.7 rows/s) 100000/324120 done (in 14 secs, 714.3 rows/s) 110000/324120 done (in 16 secs, 625.0 rows/s) 120000/324120 done (in 15 secs, 666.7 rows/s) 130000/324120 done (in 14 secs, 714.3 rows/s) 140000/324120 done (in 15 secs, 666.7 rows/s) 150000/324120 done (in 15 secs, 666.7 rows/s) 160000/324120 done (in 14 secs, 714.3 rows/s) 170000/324120 done (in 14 secs, 714.3 rows/s) 180000/324120 done (in 15 secs, 666.7 rows/s) 190000/324120 done (in 15 secs, 666.7 rows/s) 200000/324120 done (in 14 secs, 714.3 rows/s) 210000/324120 done (in 15 secs, 666.7 rows/s) 220000/324120 done (in 14 secs, 714.3 rows/s) 230000/324120 done (in 15 secs, 666.7 rows/s) failed to insert node (281015;281015;3817;species;1;1): Error writing file '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. # =================================================== -- Best Regards, Seth Johnson Senior Bioinformatics Associate Ph: (202) 470-0900 Fx: (775) 251-0358 From johnson.biotech at gmail.com Wed Sep 13 17:43:45 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Wed, 13 Sep 2006 13:43:45 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: References: Message-ID: That would be strange since I've tried it on Sun Solaris and Windows XP (with gigs of free space) with same exact results. On 9/13/06, aaron.j.mackey at gsk.com wrote: > > Most likely you've run out of space in /var/tmp ... > > -Aaron > > biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM: > > > Hello, > > I'm a newbie to BioSQl, trying to set it up on mySQL server following > the > > installation directions and ran into a problem. When trying to load the > > taxonomic info, I get an error at 230000+ line. Progress dump follows. > > Have I missed anything??? > > ======================================= > > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port 3306 > > -dbuser root -dbpass xxxxx -verbose=2 -download > > Loading NCBI taxon database in taxdata: > > ... retrieving all taxon nodes in the database > > ... reading in taxon nodes from nodes.dmp > > ... insert / update / delete taxon nodes > > 10000/324120 done (in 15 secs, 666.7 rows/s) > > 20000/324120 done (in 15 secs, 666.7 rows/s) > > 30000/324120 done (in 15 secs, 666.7 rows/s) > > 40000/324120 done (in 15 secs, 666.7 rows/s) > > 50000/324120 done (in 15 secs, 666.7 rows/s) > > 60000/324120 done (in 14 secs, 714.3 rows/s) > > 70000/324120 done (in 15 secs, 666.7 rows/s) > > 80000/324120 done (in 14 secs, 714.3 rows/s) > > 90000/324120 done (in 15 secs, 666.7 rows/s) > > 100000/324120 done (in 14 secs, 714.3 rows/s) > > 110000/324120 done (in 16 secs, 625.0 rows/s) > > 120000/324120 done (in 15 secs, 666.7 rows/s) > > 130000/324120 done (in 14 secs, 714.3 rows/s) > > 140000/324120 done (in 15 secs, 666.7 rows/s) > > 150000/324120 done (in 15 secs, 666.7 rows/s) > > 160000/324120 done (in 14 secs, 714.3 rows/s) > > 170000/324120 done (in 14 secs, 714.3 rows/s) > > 180000/324120 done (in 15 secs, 666.7 rows/s) > > 190000/324120 done (in 15 secs, 666.7 rows/s) > > 200000/324120 done (in 14 secs, 714.3 rows/s) > > 210000/324120 done (in 15 secs, 666.7 rows/s) > > 220000/324120 done (in 14 secs, 714.3 rows/s) > > 230000/324120 done (in 15 secs, 666.7 rows/s) > > failed to insert node (281015;281015;3817;species;1;1): Error writing > file > > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. > > # > > =================================================== > > > > > > -- > > Best Regards, > > > > > > Seth Johnson > > Senior Bioinformatics Associate > > > > Ph: (202) 470-0900 > > Fx: (775) 251-0358 > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > -- Best Regards, Seth Johnson Senior Bioinformatics Associate Ph: (202) 470-0900 Fx: (775) 251-0358 From hlapp at gmx.net Wed Sep 13 17:47:44 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Sep 2006 13:47:44 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: References: Message-ID: <47430222-BE83-495D-8CF0-98E9B2B8C98E@gmx.net> This looks like an issue with your mysql server to me. Maybe you are running out of diskspace or exceeding your quota? -hilmar On Sep 13, 2006, at 11:06 AM, Seth Johnson wrote: > Hello, > I'm a newbie to BioSQl, trying to set it up on mySQL server > following the > installation directions and ran into a problem. When trying to > load the > taxonomic info, I get an error at 230000+ line. Progress dump > follows. > Have I missed anything??? > ======================================= > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port > 3306 > -dbuser root -dbpass xxxxx -verbose=2 -download > Loading NCBI taxon database in taxdata: > ... retrieving all taxon nodes in the database > ... reading in taxon nodes from nodes.dmp > ... insert / update / delete taxon nodes > 10000/324120 done (in 15 secs, 666.7 rows/s) > 20000/324120 done (in 15 secs, 666.7 rows/s) > 30000/324120 done (in 15 secs, 666.7 rows/s) > 40000/324120 done (in 15 secs, 666.7 rows/s) > 50000/324120 done (in 15 secs, 666.7 rows/s) > 60000/324120 done (in 14 secs, 714.3 rows/s) > 70000/324120 done (in 15 secs, 666.7 rows/s) > 80000/324120 done (in 14 secs, 714.3 rows/s) > 90000/324120 done (in 15 secs, 666.7 rows/s) > 100000/324120 done (in 14 secs, 714.3 rows/s) > 110000/324120 done (in 16 secs, 625.0 rows/s) > 120000/324120 done (in 15 secs, 666.7 rows/s) > 130000/324120 done (in 14 secs, 714.3 rows/s) > 140000/324120 done (in 15 secs, 666.7 rows/s) > 150000/324120 done (in 15 secs, 666.7 rows/s) > 160000/324120 done (in 14 secs, 714.3 rows/s) > 170000/324120 done (in 14 secs, 714.3 rows/s) > 180000/324120 done (in 15 secs, 666.7 rows/s) > 190000/324120 done (in 15 secs, 666.7 rows/s) > 200000/324120 done (in 14 secs, 714.3 rows/s) > 210000/324120 done (in 15 secs, 666.7 rows/s) > 220000/324120 done (in 14 secs, 714.3 rows/s) > 230000/324120 done (in 15 secs, 666.7 rows/s) > failed to insert node (281015;281015;3817;species;1;1): Error > writing file > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. > # > =================================================== > > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > > Ph: (202) 470-0900 > Fx: (775) 251-0358 > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Wed Sep 13 18:00:29 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Sep 2006 14:00:29 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: References: Message-ID: <87000731-2991-490C-9824-7AAAAACE8F8C@gmx.net> Well I don't know about your systems but as a matter of fact it is a mysql error that is reported here, so it is clearly the mysql server which is causing the issue. When you say you've tried on different platforms, did you only run the script on different platforms or did you also install and set up and use the mysql server on the different (local) platforms? -hilmar On Sep 13, 2006, at 1:43 PM, Seth Johnson wrote: > That would be strange since I've tried it on Sun Solaris and > Windows XP > (with gigs of free space) with same exact results. > > On 9/13/06, aaron.j.mackey at gsk.com wrote: >> >> Most likely you've run out of space in /var/tmp ... >> >> -Aaron >> >> biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM: >> >>> Hello, >>> I'm a newbie to BioSQl, trying to set it up on mySQL server >>> following >> the >>> installation directions and ran into a problem. When trying to >>> load the >>> taxonomic info, I get an error at 230000+ line. Progress dump >>> follows. >>> Have I missed anything??? >>> ======================================= >>> # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost - >>> port 3306 >>> -dbuser root -dbpass xxxxx -verbose=2 -download >>> Loading NCBI taxon database in taxdata: >>> ... retrieving all taxon nodes in the database >>> ... reading in taxon nodes from nodes.dmp >>> ... insert / update / delete taxon nodes >>> 10000/324120 done (in 15 secs, 666.7 rows/s) >>> 20000/324120 done (in 15 secs, 666.7 rows/s) >>> 30000/324120 done (in 15 secs, 666.7 rows/s) >>> 40000/324120 done (in 15 secs, 666.7 rows/s) >>> 50000/324120 done (in 15 secs, 666.7 rows/s) >>> 60000/324120 done (in 14 secs, 714.3 rows/s) >>> 70000/324120 done (in 15 secs, 666.7 rows/s) >>> 80000/324120 done (in 14 secs, 714.3 rows/s) >>> 90000/324120 done (in 15 secs, 666.7 rows/s) >>> 100000/324120 done (in 14 secs, 714.3 rows/s) >>> 110000/324120 done (in 16 secs, 625.0 rows/s) >>> 120000/324120 done (in 15 secs, 666.7 rows/s) >>> 130000/324120 done (in 14 secs, 714.3 rows/s) >>> 140000/324120 done (in 15 secs, 666.7 rows/s) >>> 150000/324120 done (in 15 secs, 666.7 rows/s) >>> 160000/324120 done (in 14 secs, 714.3 rows/s) >>> 170000/324120 done (in 14 secs, 714.3 rows/s) >>> 180000/324120 done (in 15 secs, 666.7 rows/s) >>> 190000/324120 done (in 15 secs, 666.7 rows/s) >>> 200000/324120 done (in 14 secs, 714.3 rows/s) >>> 210000/324120 done (in 15 secs, 666.7 rows/s) >>> 220000/324120 done (in 14 secs, 714.3 rows/s) >>> 230000/324120 done (in 15 secs, 666.7 rows/s) >>> failed to insert node (281015;281015;3817;species;1;1): Error >>> writing >> file >>> '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. >>> # >>> =================================================== >>> >>> >>> -- >>> Best Regards, >>> >>> >>> Seth Johnson >>> Senior Bioinformatics Associate >>> >>> Ph: (202) 470-0900 >>> Fx: (775) 251-0358 >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >> >> >> > > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > > Ph: (202) 470-0900 > Fx: (775) 251-0358 > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From johnson.biotech at gmail.com Wed Sep 13 18:01:16 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Wed, 13 Sep 2006 14:01:16 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: References: Message-ID: Sorry, it didn't occur to me that running out of space was MySQL related. :) On 9/13/06, aaron.j.mackey at gsk.com wrote: > > strange or not, that is exactly what MySQL error 28 means: no space left > on device. > > -Aaron > > "Seth Johnson" wrote on 09/13/2006 01:43:45 > PM: > > > That would be strange since I've tried it on Sun Solaris and Windows > > XP (with gigs of free space) with same exact results. > > > On 9/13/06, aaron.j.mackey at gsk.com wrote: > > Most likely you've run out of space in /var/tmp ... > > > > -Aaron > > > > biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM: > > > > > Hello, > > > I'm a newbie to BioSQl, trying to set it up on mySQL server following > > the > > > installation directions and ran into a problem. When trying to load > the > > > taxonomic info, I get an error at 230000+ line. Progress dump > follows. > > > Have I missed anything??? > > > ======================================= > > > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port > 3306 > > > -dbuser root -dbpass xxxxx -verbose=2 -download > > > Loading NCBI taxon database in taxdata: > > > ... retrieving all taxon nodes in the database > > > ... reading in taxon nodes from nodes.dmp > > > ... insert / update / delete taxon nodes > > > 10000/324120 done (in 15 secs, 666.7 rows/s) > > > 20000/324120 done (in 15 secs, 666.7 rows/s) > > > 30000/324120 done (in 15 secs, 666.7 rows/s) > > > 40000/324120 done (in 15 secs, 666.7 rows/s) > > > 50000/324120 done (in 15 secs, 666.7 rows/s) > > > 60000/324120 done (in 14 secs, 714.3 rows/s) > > > 70000/324120 done (in 15 secs, 666.7 rows/s) > > > 80000/324120 done (in 14 secs, 714.3 rows/s) > > > 90000/324120 done (in 15 secs, 666.7 rows/s) > > > 100000/324120 done (in 14 secs, 714.3 rows/s) > > > 110000/324120 done (in 16 secs, 625.0 rows/s) > > > 120000/324120 done (in 15 secs, 666.7 rows/s) > > > 130000/324120 done (in 14 secs, 714.3 rows/s) > > > 140000/324120 done (in 15 secs, 666.7 rows/s) > > > 150000/324120 done (in 15 secs, 666.7 rows/s) > > > 160000/324120 done (in 14 secs, 714.3 rows/s) > > > 170000/324120 done (in 14 secs, 714.3 rows/s) > > > 180000/324120 done (in 15 secs, 666.7 rows/s) > > > 190000/324120 done (in 15 secs, 666.7 rows/s) > > > 200000/324120 done (in 14 secs, 714.3 rows/s) > > > 210000/324120 done (in 15 secs, 666.7 rows/s) > > > 220000/324120 done (in 14 secs, 714.3 rows/s) > > > 230000/324120 done (in 15 secs, 666.7 rows/s) > > > failed to insert node (281015;281015;3817;species;1;1): Error writing > > file > > > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. > > > # > > > =================================================== > > > > > > > > > -- > > > Best Regards, > > > > > > > > > Seth Johnson > > > Senior Bioinformatics Associate > > > > > > Ph: (202) 470-0900 > > > Fx: (775) 251-0358 > > > _______________________________________________ > > > BioSQL-l mailing list > > > BioSQL-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > > > > > > > > > > -- > > Best Regards, > > > > > > Seth Johnson > > Senior Bioinformatics Associate > > > > Ph: (202) 470-0900 > > Fx: (775) 251-0358 > > -- Best Regards, Seth Johnson Senior Bioinformatics Associate Ph: (202) 470-0900 Fx: (775) 251-0358 From aaron.j.mackey at gsk.com Wed Sep 13 16:27:44 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Wed, 13 Sep 2006 12:27:44 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: Message-ID: Most likely you've run out of space in /var/tmp ... -Aaron biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM: > Hello, > I'm a newbie to BioSQl, trying to set it up on mySQL server following the > installation directions and ran into a problem. When trying to load the > taxonomic info, I get an error at 230000+ line. Progress dump follows. > Have I missed anything??? > ======================================= > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port 3306 > -dbuser root -dbpass xxxxx -verbose=2 -download > Loading NCBI taxon database in taxdata: > ... retrieving all taxon nodes in the database > ... reading in taxon nodes from nodes.dmp > ... insert / update / delete taxon nodes > 10000/324120 done (in 15 secs, 666.7 rows/s) > 20000/324120 done (in 15 secs, 666.7 rows/s) > 30000/324120 done (in 15 secs, 666.7 rows/s) > 40000/324120 done (in 15 secs, 666.7 rows/s) > 50000/324120 done (in 15 secs, 666.7 rows/s) > 60000/324120 done (in 14 secs, 714.3 rows/s) > 70000/324120 done (in 15 secs, 666.7 rows/s) > 80000/324120 done (in 14 secs, 714.3 rows/s) > 90000/324120 done (in 15 secs, 666.7 rows/s) > 100000/324120 done (in 14 secs, 714.3 rows/s) > 110000/324120 done (in 16 secs, 625.0 rows/s) > 120000/324120 done (in 15 secs, 666.7 rows/s) > 130000/324120 done (in 14 secs, 714.3 rows/s) > 140000/324120 done (in 15 secs, 666.7 rows/s) > 150000/324120 done (in 15 secs, 666.7 rows/s) > 160000/324120 done (in 14 secs, 714.3 rows/s) > 170000/324120 done (in 14 secs, 714.3 rows/s) > 180000/324120 done (in 15 secs, 666.7 rows/s) > 190000/324120 done (in 15 secs, 666.7 rows/s) > 200000/324120 done (in 14 secs, 714.3 rows/s) > 210000/324120 done (in 15 secs, 666.7 rows/s) > 220000/324120 done (in 14 secs, 714.3 rows/s) > 230000/324120 done (in 15 secs, 666.7 rows/s) > failed to insert node (281015;281015;3817;species;1;1): Error writing file > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. > # > =================================================== > > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > > Ph: (202) 470-0900 > Fx: (775) 251-0358 > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > From aaron.j.mackey at gsk.com Wed Sep 13 17:49:58 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Wed, 13 Sep 2006 13:49:58 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: Message-ID: strange or not, that is exactly what MySQL error 28 means: no space left on device. -Aaron "Seth Johnson" wrote on 09/13/2006 01:43:45 PM: > That would be strange since I've tried it on Sun Solaris and Windows > XP (with gigs of free space) with same exact results. > On 9/13/06, aaron.j.mackey at gsk.com wrote: > Most likely you've run out of space in /var/tmp ... > > -Aaron > > biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM: > > > Hello, > > I'm a newbie to BioSQl, trying to set it up on mySQL server following > the > > installation directions and ran into a problem. When trying to load the > > taxonomic info, I get an error at 230000+ line. Progress dump follows. > > Have I missed anything??? > > ======================================= > > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port 3306 > > -dbuser root -dbpass xxxxx -verbose=2 -download > > Loading NCBI taxon database in taxdata: > > ... retrieving all taxon nodes in the database > > ... reading in taxon nodes from nodes.dmp > > ... insert / update / delete taxon nodes > > 10000/324120 done (in 15 secs, 666.7 rows/s) > > 20000/324120 done (in 15 secs, 666.7 rows/s) > > 30000/324120 done (in 15 secs, 666.7 rows/s) > > 40000/324120 done (in 15 secs, 666.7 rows/s) > > 50000/324120 done (in 15 secs, 666.7 rows/s) > > 60000/324120 done (in 14 secs, 714.3 rows/s) > > 70000/324120 done (in 15 secs, 666.7 rows/s) > > 80000/324120 done (in 14 secs, 714.3 rows/s) > > 90000/324120 done (in 15 secs, 666.7 rows/s) > > 100000/324120 done (in 14 secs, 714.3 rows/s) > > 110000/324120 done (in 16 secs, 625.0 rows/s) > > 120000/324120 done (in 15 secs, 666.7 rows/s) > > 130000/324120 done (in 14 secs, 714.3 rows/s) > > 140000/324120 done (in 15 secs, 666.7 rows/s) > > 150000/324120 done (in 15 secs, 666.7 rows/s) > > 160000/324120 done (in 14 secs, 714.3 rows/s) > > 170000/324120 done (in 14 secs, 714.3 rows/s) > > 180000/324120 done (in 15 secs, 666.7 rows/s) > > 190000/324120 done (in 15 secs, 666.7 rows/s) > > 200000/324120 done (in 14 secs, 714.3 rows/s) > > 210000/324120 done (in 15 secs, 666.7 rows/s) > > 220000/324120 done (in 14 secs, 714.3 rows/s) > > 230000/324120 done (in 15 secs, 666.7 rows/s) > > failed to insert node (281015;281015;3817;species;1;1): Error writing > file > > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545. > > # > > =================================================== > > > > > > -- > > Best Regards, > > > > > > Seth Johnson > > Senior Bioinformatics Associate > > > > Ph: (202) 470-0900 > > Fx: (775) 251-0358 > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biosql-l > > > > > > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > > Ph: (202) 470-0900 > Fx: (775) 251-0358 From gwu at molbio.mgh.harvard.edu Wed Sep 27 01:33:38 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 26 Sep 2006 21:33:38 -0400 Subject: [BioSQL-l] load_ncbi_taxonomy.pl error In-Reply-To: References: Message-ID: <4519D4F2.4060001@molbio.mgh.harvard.edu> Hi Everyone, I finally finished loading some Genbank genome sequences(Arabidopsis thaliana and C. elegans) into my MySQL(5.0.19 on Redhad AS 4) BioSQL database though the load_seqdatabase.pl works extremely slow(If -debug is turned on, a lot of messages about not able to find adaptor class for Bio::Annotation::TypeManager. Is this about the dynamic library loading issue mention in one of Hilmar's message?). Now I'm writing views and stored procedures so other projects can easily retrieve specific information. But so far I have not figured out how to write a SQL statement to list all genes of the genomes. Can anyone show me how to get the information or let me know where to find related document? Thanks in advance. Gang From gwu at molbio.mgh.harvard.edu Wed Sep 27 13:53:21 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Wed, 27 Sep 2006 09:53:21 -0400 Subject: [BioSQL-l] how to retrieve specific information from BioSQL database In-Reply-To: <4519D4F2.4060001@molbio.mgh.harvard.edu> References: <4519D4F2.4060001@molbio.mgh.harvard.edu> Message-ID: <451A8251.5060302@molbio.mgh.harvard.edu> Hi Everyone, I finally finished loading some Genbank genome sequences(Arabidopsis thaliana and C. elegans) into my MySQL(5.0.19 on Redhad AS 4) BioSQL database though the load_seqdatabase.pl works extremely slow(If -debug is turned on, a lot of messages about not able to find adaptor class for Bio::Annotation::TypeManager. Is this about the dynamic library loading issue mention in one of Hilmar's message?). Now I'm writing views and stored procedures so other projects can easily retrieve specific information. But so far I have not figured out how to write a SQL statement to list all genes of the genomes. Can anyone show me how to get the information or let me know where to find related document? Thanks in advance. Gang From johnson.biotech at gmail.com Wed Sep 27 17:39:05 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Wed, 27 Sep 2006 13:39:05 -0400 Subject: [BioSQL-l] Error retrieving sequence from BioSQL Message-ID: Hello guys, I successfully populated the biosql database, thanks to you. Now, I'm trying to retrieve a sequence from it following the example from BOSC2003 slides and ran into uninformative error (at least to me it doesn't mean anyting). I suspect that I'm missing something and hope you can point me in the right direction. Here's my source code: ------------------------------------------------------------------------- #!/usr/bin/perl -w use strict; use warnings; use Bio::Seq; use Bio::Seq::SeqFactory; use Bio::DB::SimpleDBContext; use Bio::DB::BioDB; my $dbc = Bio::DB::SimpleDBContext->new( -driver => 'mysql', -dbname => 'BioSQL_1', -host => '192.168.1.3', -user => 'xxxxx', -pass => 'xxxxxx' ); my $db = Bio::DB::BioDB->new(-database => 'biosql', -dbcontext => $dbc); my $seq = Bio::Seq->new(-accession_number => 'NM_014580', -namespace => 'refseq_H_sapiens'); my $seqfact = Bio::Seq::SeqFactory->new(-type => 'Bio::Seq'); my $adp = $db->get_object_adaptor($seq); my $dbseq = $adp->find_by_unique_key($seq, -obj_factory => $seqfact); my $out = Bio::SeqIO->newFh('-format' => 'EMBL'); print $out $dbseq; exit; ----------------------------------------------------------------- Just when the "find_by_unique_key" function is executed I get the following error: ================================ Undefined subroutine &Bio::Root::Root::throw called at c:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm line 199. ================================ The sequence does exist in the database. I checked that. Any ideas??? -- Best Regards, Seth Johnson Senior Bioinformatics Associate