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[Genbank-bb] GenBank Update Problem : 0131 : Corrupted con_nc.0131.flat.gz update file

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Jan 31 17:18:03 EST 2014


Greetings GenBank Users,

The flatfile version of the "CON division" GenBank Incremental Update
(GIU) product for January 31 2014 contained corrupted CONTIG lines.

The affected file is con_nc.0131.flat.gz :

ftp> pwd
257 "/genbank/daily-nc" is the current directory

ftp> dir con*0131*
227 Entering Passive Mode (130,14,29,30,174,245)
150 Opening ASCII mode data connection for file list
-r--r--r--   1 ftp      anonymous 10185707 Jan 31 07:23 con_nc.0131.flat.gz


Here is an excerpt from one of the impacted records:

LOCUS       KI965806              507403 bp    DNA     linear   CON 30-JAN-2014
DEFINITION  Vibrio parahaemolyticus 861 genomic scaffold vp861.contig.3, whole
            genome shotgun sequence.
ACCESSION   KI965806 AZGV01000000
VERSION     KI965806.1  GI:576999502
DBLINK      BioProject: PRJNA176635
            BioSample: SAMN01923894
....
....
CONTIG      join(AZGV01000053.1:1..21754,gap(160),JF^C<B2>8I
            ^O<9B>IF.1:1..54538,gap(140),AZGV01000055.1:1..36601,gap(132),
            AZGV01000056.1:1..23688,gap(138),AZGV01000057.1:1..50396,gap(118),
            AZGV01000058.1:1..63282,gap(124),AZGV01000059.1:1..12525,gap(138),
            AZGV01000060.1:1..17934,gap(130),AZGV01000061.1:1..25377,gap(153),
            AZGV01000062.1:1..144594,gap(186),AZGV01000063.1:1..21038,gap(113),
            AZGV01000064.1:1..15590,gap(133),AZGV01000065.1:1..18421)
//

A total of 14 records were affected:

KI965783
KI965786
KI965786
KI965795
KI965806
KI965817
KI965886
KI965887
KI965888
KI965889
KI965890
KI965892
KI965899
KI965906

The ASN.1 version of the 0131 CON-division GIU was not affected.

A system responsible for GI->Accession.Version mapping experienced
a hardware failure, and the fail-over system wasn't properly 
configured to handle sequences that were de-novo or changed.
Work is underway to improve the fail-over's reliability.

We have decided to redistribute every CON-division/scaffold record
from the January 31 update, via tomorrow's February 1 GIU. This
should ensure that those who are processing the incrementals will see
and process the corrected versions of the corrupted records.

We would like to once again thank GenBank users at Chemical Abstracts
Services (www.cas.org) for alerting us to this problem. We appreciate
the scrutiny of the GIU that our users provide, and appreciate problem
reports.

Our apologies for any inconvenience that this may have caused.

Mark Cavanaugh
GenBank
NCBI/NLM/NIH/HHS





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