dbiflat dies...can I restart where it left off?
Wiepert, Mathieu
Wiepert.Mathieu at mayo.edu
Tue Mar 25 16:05:35 UTC 2003
Hi,
I am trying to index a large set of est genbank files with dbiflat. After a few hours of processing, I got
Index a flat file database
EMBL : EMBL
SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
GB : Genbank, DDBJ
REFSEQ : Refseq
Entry format [SWISS]: genbank
Database directory [.]:
Wildcard database filename [*.dat]: *.genbank
Database name: test
Release number [0.0]: .1
Index date [00/00/00]: 03/25/03
Warning: Duplicate ID skipped: 'BF291273' All hits will point to first ID found
EMBOSS An error in embdbi.c at line 1074:
Error in embDbiSortWriteFields, expected entry BU664328 not found
Is there a way to restart this? I didn't use any of the -warning -error -fatal -die -debug options, maybe I should have, so I could see a log. I thought this might be one way to index genbank itself? I have tried bioperl for this, but it takes MUCH longer (as I might have suspected anyway). Haven't tried anything from the ncbi toolkit.
-Mat
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