dbiflat dies...can I restart where it left off?

Wiepert, Mathieu Wiepert.Mathieu at mayo.edu
Tue Mar 25 16:05:35 UTC 2003


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.


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