Problem indexing EMBL

[Carlos Javier]

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.

[James Abbott]

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