Problem indexing EMBL

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2 total messages Started by Carlos Javier Tue, 21 Sep 2004 17:44

#89

Author: Carlos Javier
Date: Tue, 21 Sep 2004 17:44

16 lines
1990 bytes

I found this problem indexing EMBL database:

> Creating sort set for the div field of embl
> Creating sort set for the acc field of embl
> /gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i:100: error: 
> Fatal internal error
>   Reason: "NULL lib pointer", file: "library.c", line:4838
> gmake: *** [EMBL/EMBL_sort.acc.pacc] Error 255
> /gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i -libName EMBL 
> -fldName 'pac' -odir /gfs/srs/srs7.1.3/srs_tmp/srs/index/
> /gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i:100: error: 
> Fatal internal error
>   Reason: "NULL lib pointer", file: "library.c", line:4838

Does anyone know what is happening here??
I'm using SRS7.1.3 and EMBL Release 79.

Re: Problem indexing EMBL

#91

Author: James Abbott
Date: Tue, 05 Oct 2004 16:27

35 lines
3070 bytes

Hi Carlos,

Carlos Javier wrote:

>>Creating sort set for the div field of embl
>>Creating sort set for the acc field of embl
>>/gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i:100: error: 
>>Fatal internal error
>>  Reason: "NULL lib pointer", file: "library.c", line:4838
>>gmake: *** [EMBL/EMBL_sort.acc.pacc] Error 255
>>/gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i -libName EMBL 
>>-fldName 'pac' -odir /gfs/srs/srs7.1.3/srs_tmp/srs/index/
>>/gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i:100: error: 
>>Fatal internal error
>>  Reason: "NULL lib pointer", file: "library.c", line:4838

 From memory, you get this error when building a virtual library if you 
do not have all the 'member libraries' of the virtual libary enabled on 
your system. The Library definition for EMBL (look for the $EMBL_DB 
section at the top of $SRSDB/embl.i) contains a list of the databases 
which make up the EMBL virtual library:

  memberLibs:{
       $EMBLREL_DB
       $EMBLNEW_DB
       $EMBLCONT_DB
       $EMBLWGS_DB
     }

If you do not use the EMBL WGS, new or Contig databases, try commenting 
  these out of the list of memberLibs, then run srssection. Then try 
rerunning srscheck/srsdo, and see if that solves the problem.

Hope that helps,
James

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