From owner-genbankb@hgmp.mrc.ac.uk Wed Sep 6 05:46:58 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C9F1717B0F; Wed, 6 Sep 2000 05:46:57 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id B4DB617B10; Wed, 6 Sep 2000 05:46:55 +0100 (BST) To: genbank@net.bio.net Newsgroups: bionet.molbio.genbank Date: Wed, 06 Sep 2000 00:11:11 GMT From: Bradley K.Sherman Subject: Entrez linking broken Message-Id: <20000906044655.B4DB617B10@mercury.hgmp.mrc.ac.uk> Sender: owner-genbankb@hgmp.mrc.ac.uk Precedence: bulk ** ** Comment from the moderator: ** Problems like this are best forwarded to NCBI directly, ** but _also_ appropriate for this newsgroup. ** NCBI help can be reached at: info@ncbi.nlm.nih.gov ** cheers, francis@cmmt.ubc.ca ** ---> Search [Protein] for [2443890] [click Go] [click AAB71483] Gives error: "Query number not found: #1" There are other problems today, but let's start with this one. --bks - gttaacaattaaagagtgtttatcgaaattcattatatagtggtttatatagaccacttc - - GenBank newsgroup see: http://www.bio.net/hypermail/genbankb/ - GENBANKB e-mail: messages sent to genbankb@net.bio.net - subscribe: e-mail biosci-server@net.bio.net with: subscribe genbankb - unsub: e-mail biosci-server@net.bio.net with: unsubscribe genbankb - GenBank on the WWW, see: http://www.ncbi.nlm.nih.gov/Genbank/ - problems with GENBANKB? E-mail moderator: francis@cmmt.ubc.ca From owner-genbankb@hgmp.mrc.ac.uk Thu Sep 7 09:02:00 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D605717B78; Thu, 7 Sep 2000 09:01:59 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 2389B17B68; Thu, 7 Sep 2000 09:01:58 +0100 (BST) To: genbank@net.bio.net Newsgroups: bionet.molbio.genbank Date: Wed, 06 Sep 2000 17:09:32 GMT From: Bradley K.Sherman Subject: Re: Entrez linking broken Message-Id: <20000907080158.2389B17B68@mercury.hgmp.mrc.ac.uk> Sender: owner-genbankb@hgmp.mrc.ac.uk Precedence: bulk In article <8p4i7u$t0g$1@mercury.hgmp.mrc.ac.uk>, Bradley K. Sherman wrote: > >** >** Comment from the moderator: >** Problems like this are best forwarded to NCBI directly, >** but _also_ appropriate for this newsgroup. >** NCBI help can be reached at: info@ncbi.nlm.nih.gov >** cheers, francis@cmmt.ubc.ca >** Yes I also sent mail to one of the various addresses listed for help on the NCBI pages. I would have to say that the response from NCBI was a bit cryptic, so I'm offering another pathological example here: Do a default Basic BLAST on the following sequence: >fakefasta created Wed Sep 6 09:48:48 PDT 2000 AGANGAACAAGACAAGAAGAACAAAGTACCCAAGAAAATACACAAGAAGGAAACACAAAG ATTGATATTGATCCAAAAGCAATGGCGTACGAGAAAGTCAACGAGCTTAACCTTAAGGAC ACAGAGCTATGTCTTGGATTACCCGGAAGAACAGAGAAGATCAAAGAAGAACAAGAGGTT TCTTGCGTTATTTGTAACAACAAGCGTCTATTTGAGGAAACTCGTGATGAAGAAGAATCT ACACCTCCTACCAAAACTCAAATCGTTGGTTGGCCACCAGTGAGATCTTCCCGTAAGAAC AACAACAGTGTGAGCTACGTGAAAGTGAGTATGGCGGAGCTCCTTACCTTCGCAAGATCG ATCTCAAGACATACAAAAACTACCCCGAGCTTCTCAAAGCGNTAGAGAATATGTTCAAAG NCATGATTGGNGAATATTGNGAGAGAGAAGGATACAAAAGGATCTGGATTTGTCCCACAT ACCAAGAAAAAGANGGGGACTGGATGTTGGGTGGGGA When the results arrive, scroll down to to the best hit, gb|L15449.1|ATHIAA2A And click on it to get another "Query number not found:#1" error message. --bks - gttaacaattaaagagtgtttatcgaaattcattatatagtggtttatatagaccacttc - - GenBank newsgroup see: http://www.bio.net/hypermail/genbankb/ - GENBANKB e-mail: messages sent to genbankb@net.bio.net - subscribe: e-mail biosci-server@net.bio.net with: subscribe genbankb - unsub: e-mail biosci-server@net.bio.net with: unsubscribe genbankb - GenBank on the WWW, see: http://www.ncbi.nlm.nih.gov/Genbank/ - problems with GENBANKB? E-mail moderator: francis@cmmt.ubc.ca From owner-genbankb@hgmp.mrc.ac.uk Thu Sep 7 17:32:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 687B617B6F; Thu, 7 Sep 2000 17:32:28 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id EDD1017B7F; Thu, 7 Sep 2000 17:32:26 +0100 (BST) To: genbank@net.bio.net Newsgroups: bionet.molbio.genbank Date: 7 Sep 2000 15:46:42 +0100 From: Mark Cavanaugh Subject: Re: Entrez linking broken Message-Id: <20000907163226.EDD1017B7F@mercury.hgmp.mrc.ac.uk> Sender: owner-genbankb@hgmp.mrc.ac.uk Precedence: bulk A fairly major change was made to Entrez recently. Although extensive testing was done, it is always difficult to simulate the effects of proxies, load balancing, and very heavy user load. Unfortunately, under just those conditions, a problem was discovered with the new software. So the change was backed out late Wednesday. Clicking on the hit for L15449 in the results of the BLAST search you describe now behaves properly. If the responses from NCBI service addresses were unclear, this could be due in part to the fact that the cause of the problem was quite difficult to determine. All the details weren't known until late yesterday.... --mark cavanaugh > To: genbank@net.bio.net > Date: Wed, 06 Sep 2000 17:09:32 GMT > From: "Bradley K.Sherman" > Subject: Re: Entrez linking broken > > In article <8p4i7u$t0g$1@mercury.hgmp.mrc.ac.uk>, > Bradley K. Sherman wrote: > > > >** > >** Comment from the moderator: > >** Problems like this are best forwarded to NCBI directly, > >** but _also_ appropriate for this newsgroup. > >** NCBI help can be reached at: info@ncbi.nlm.nih.gov > >** cheers, francis@cmmt.ubc.ca > >** > > Yes I also sent mail to one of the various addresses > listed for help on the NCBI pages. I would have to > say that the response from NCBI was a bit cryptic, so > I'm offering another pathological example here: > > Do a default Basic BLAST > > on the following sequence: > > >fakefasta created Wed Sep 6 09:48:48 PDT 2000 > AGANGAACAAGACAAGAAGAACAAAGTACCCAAGAAAATACACAAGAAGGAAACACAAAG > ATTGATATTGATCCAAAAGCAATGGCGTACGAGAAAGTCAACGAGCTTAACCTTAAGGAC > ACAGAGCTATGTCTTGGATTACCCGGAAGAACAGAGAAGATCAAAGAAGAACAAGAGGTT > TCTTGCGTTATTTGTAACAACAAGCGTCTATTTGAGGAAACTCGTGATGAAGAAGAATCT > ACACCTCCTACCAAAACTCAAATCGTTGGTTGGCCACCAGTGAGATCTTCCCGTAAGAAC > AACAACAGTGTGAGCTACGTGAAAGTGAGTATGGCGGAGCTCCTTACCTTCGCAAGATCG > ATCTCAAGACATACAAAAACTACCCCGAGCTTCTCAAAGCGNTAGAGAATATGTTCAAAG > NCATGATTGGNGAATATTGNGAGAGAGAAGGATACAAAAGGATCTGGATTTGTCCCACAT > ACCAAGAAAAAGANGGGGACTGGATGTTGGGTGGGGA > > When the results arrive, scroll down to to the best hit, > > gb|L15449.1|ATHIAA2A > > And click on it to get another "Query number not found:#1" > error message. > > --bks > > > > - gttaacaattaaagagtgtttatcgaaattcattatatagtggtttatatagaccacttc > - > - GenBank newsgroup see: http://www.bio.net/hypermail/genbankb/ > - GENBANKB e-mail: messages sent to genbankb@net.bio.net > - subscribe: e-mail biosci-server@net.bio.net with: subscribe genbankb > - unsub: e-mail biosci-server@net.bio.net with: unsubscribe genbankb > - GenBank on the WWW, see: http://www.ncbi.nlm.nih.gov/Genbank/ > - problems with GENBANKB? E-mail moderator: francis@cmmt.ubc.ca > > > > --- From owner-genbankb@hgmp.mrc.ac.uk Thu Sep 7 17:32:54 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 16AAF17B12; Thu, 7 Sep 2000 17:32:53 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 7CA3717B6F; Thu, 7 Sep 2000 17:32:52 +0100 (BST) To: genbank@net.bio.net Newsgroups: bionet.molbio.genbank Date: Thu, 07 Sep 2000 16:12:47 GMT From: Bradley K.Sherman Subject: Re: Entrez linking broken (Now fixed) Message-Id: <20000907163252.7CA3717B6F@mercury.hgmp.mrc.ac.uk> Sender: owner-genbankb@hgmp.mrc.ac.uk Precedence: bulk >And click on it to get another "Query number not found:#1" These problems have been resolved. --bks - gttaacaattaaagagtgtttatcgaaattcattatatagtggtttatatagaccacttc - - GenBank newsgroup see: http://www.bio.net/hypermail/genbankb/ - GENBANKB e-mail: messages sent to genbankb@net.bio.net - subscribe: e-mail biosci-server@net.bio.net with: subscribe genbankb - unsub: e-mail biosci-server@net.bio.net with: unsubscribe genbankb - GenBank on the WWW, see: http://www.ncbi.nlm.nih.gov/Genbank/ - problems with GENBANKB? E-mail moderator: francis@cmmt.ubc.ca From owner-genbankb@hgmp.mrc.ac.uk Tue Sep 12 00:52:16 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2172717AC9; Tue, 12 Sep 2000 00:52:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 03EF917AD6; Tue, 12 Sep 2000 00:52:14 +0100 (BST) To: genbank@net.bio.net Newsgroups: bionet.molbio.genbank Date: Mon, 11 Sep 2000 23:06:28 GMT From: Bradley K.Sherman Subject: Re: Entrez linking broken (AGAIN!) Message-Id: <20000911235214.03EF917AD6@mercury.hgmp.mrc.ac.uk> Sender: owner-genbankb@hgmp.mrc.ac.uk Precedence: bulk In article <8p4i7u$t0g$1@mercury.hgmp.mrc.ac.uk>, Bradley K. Sherman wrote: > >** >** Comment from the moderator: >** Problems like this are best forwarded to NCBI directly, >** but _also_ appropriate for this newsgroup. >** NCBI help can be reached at: info@ncbi.nlm.nih.gov >** cheers, francis@cmmt.ubc.ca >** > > > > >---> Search [Protein] for [2443890] > [click Go] > > [click AAB71483] > >Gives error: "Query number not found: #1" > >There are other problems today, but let's start >with this one. As of right now, Mon Sep 11 16:06:40 PDT 2000, all of the problems have returned. (Reported to NCBI under separate cover.) --bks - gttaacaattaaagagtgtttatcgaaattcattatatagtggtttatatagaccacttc - - GenBank newsgroup see: http://www.bio.net/hypermail/genbankb/ - GENBANKB e-mail: messages sent to genbankb@net.bio.net - subscribe: e-mail biosci-server@net.bio.net with: subscribe genbankb - unsub: e-mail biosci-server@net.bio.net with: unsubscribe genbankb - GenBank on the WWW, see: http://www.ncbi.nlm.nih.gov/Genbank/ - problems with GENBANKB? E-mail moderator: francis@cmmt.ubc.ca From owner-genbankb@hgmp.mrc.ac.uk Wed Sep 13 06:22:57 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5E93217AFF; Wed, 13 Sep 2000 06:22:57 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 1D2F617B3F; Wed, 13 Sep 2000 06:22:56 +0100 (BST) To: genbank@net.bio.net Newsgroups: bionet.molbio.genbank Date: 12 Sep 2000 16:10:39 +0100 From: Mark Cavanaugh Subject: Re: Entrez linking broken (AGAIN!) Message-Id: <20000913052256.1D2F617B3F@mercury.hgmp.mrc.ac.uk> Sender: owner-genbankb@hgmp.mrc.ac.uk Precedence: bulk It appears that another attempt was made to install new Entrez software, which caused problems similar to those of last week. But the search that you describe now works as it should, no error message; so it seems that the problems have been resolved. Please continue to inform us via the NCBI helpdesk if this is not the case for you. Best regards, Mark Cavanaugh GenBank > To: genbank@net.bio.net > Date: Mon, 11 Sep 2000 23:06:28 GMT > From: "Bradley K.Sherman" > Subject: Re: Entrez linking broken (AGAIN!) > > In article <8p4i7u$t0g$1@mercury.hgmp.mrc.ac.uk>, > Bradley K. Sherman wrote: > > > >** > >** Comment from the moderator: > >** Problems like this are best forwarded to NCBI directly, > >** but _also_ appropriate for this newsgroup. > >** NCBI help can be reached at: info@ncbi.nlm.nih.gov > >** cheers, francis@cmmt.ubc.ca > >** > > > > > > > > > >---> Search [Protein] for [2443890] > > [click Go] > > > > [click AAB71483] > > > >Gives error: "Query number not found: #1" > > > >There are other problems today, but let's start > >with this one. > > As of right now, Mon Sep 11 16:06:40 PDT 2000, > all of the problems have returned. (Reported > to NCBI under separate cover.) > > --bks > --- - gttaacaattaaagagtgtttatcgaaattcattatatagtggtttatatagaccacttc - - GenBank newsgroup see: http://www.bio.net/hypermail/genbankb/ - GENBANKB e-mail: messages sent to genbankb@net.bio.net - subscribe: e-mail biosci-server@net.bio.net with: subscribe genbankb - unsub: e-mail biosci-server@net.bio.net with: unsubscribe genbankb - GenBank on the WWW, see: http://www.ncbi.nlm.nih.gov/Genbank/ - problems with GENBANKB? E-mail moderator: francis@cmmt.ubc.ca From owner-genbankb@hgmp.mrc.ac.uk Wed Sep 13 13:42:21 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C528F17B3F; Wed, 13 Sep 2000 13:42:20 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 6DB5717B49; Wed, 13 Sep 2000 13:42:19 +0100 (BST) To: genbank@net.bio.net Newsgroups: bionet.molbio.genbank Date: Wed, 13 Sep 2000 11:44:50 GMT From: Bradley K.Sherman Subject: Re: Entrez linking broken (AGAIN!) Message-Id: <20000913124219.6DB5717B49@mercury.hgmp.mrc.ac.uk> Sender: owner-genbankb@hgmp.mrc.ac.uk Precedence: bulk In article <8pn2vf$dcd$1@mercury.hgmp.mrc.ac.uk>, Mark Cavanaugh wrote: > >But the search that you describe now works as it should, Yes, it is working again now. Are we likely to see more such incidents in the near future? In particular, does this imply that some forms of Entrez hyperlink syntax are being deprecated? --bks - gttaacaattaaagagtgtttatcgaaattcattatatagtggtttatatagaccacttc - - GenBank newsgroup see: http://www.bio.net/hypermail/genbankb/ - GENBANKB e-mail: messages sent to genbankb@net.bio.net - subscribe: e-mail biosci-server@net.bio.net with: subscribe genbankb - unsub: e-mail biosci-server@net.bio.net with: unsubscribe genbankb - GenBank on the WWW, see: http://www.ncbi.nlm.nih.gov/Genbank/ - problems with GENBANKB? E-mail moderator: francis@cmmt.ubc.ca From owner-genbankb@hgmp.mrc.ac.uk Wed Sep 13 19:36:52 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4C2B717A93; Wed, 13 Sep 2000 19:36:52 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 169B517B8F; Wed, 13 Sep 2000 19:36:51 +0100 (BST) To: genbank@net.bio.net Newsgroups: bionet.molbio.genbank Date: 13 Sep 2000 19:28:07 +0100 From: Mark Cavanaugh Subject: Re: Entrez linking broken (AGAIN!) Message-Id: <20000913183651.169B517B8F@mercury.hgmp.mrc.ac.uk> Sender: owner-genbankb@hgmp.mrc.ac.uk Precedence: bulk > To: genbank@net.bio.net > Date: Wed, 13 Sep 2000 11:44:50 GMT > From: "Bradley K.Sherman" > Subject: Re: Entrez linking broken (AGAIN!) > > In article <8pn2vf$dcd$1@mercury.hgmp.mrc.ac.uk>, > Mark Cavanaugh wrote: > > > >But the search that you describe now works as it should, > > Yes, it is working again now. Are we likely to see more > such incidents in the near future? In particular, does > this imply that some forms of Entrez hyperlink syntax are > being deprecated? This problem had no implications for hyperlink syntax that I'm aware of. As far as the possibility of future incidents: Sure, similar problems could certainly arise when significant changes are made to the Entrez/PubMed system. It's very difficult to simulate the "real world" of extremely heavy loads, proxies, etc. when testing new software. NCBI *does* perform such simulations, but sometimes that simply isn't enough... Hence the install, back-out, re-install, fix scenario of the last week. But this type of scenario is pretty rare; the testing which is done is usually sufficient to catch big problems before deployment. If you find that this is *NOT* the case, we'd certainly like to know; please continue to report difficulties via the NCBI Service Desk: info@ncbi.nlm.nih.gov Regards, Mark Cavanaugh GenBank --- - gttaacaattaaagagtgtttatcgaaattcattatatagtggtttatatagaccacttc - - GenBank newsgroup see: http://www.bio.net/hypermail/genbankb/ - GENBANKB e-mail: messages sent to genbankb@net.bio.net - subscribe: e-mail biosci-server@net.bio.net with: subscribe genbankb - unsub: e-mail biosci-server@net.bio.net with: unsubscribe genbankb - GenBank on the WWW, see: http://www.ncbi.nlm.nih.gov/Genbank/ - problems with GENBANKB? E-mail moderator: francis@cmmt.ubc.ca