blastpgp error on UniProt

[vadaner]

Hello,
While running blastpgp on a newly downloaded UniProt database we get
the following error:

$ /usr/users/gcg/linuxbin/gcgbin/pub/gcg_blastpgp -i pdb1a9x.seq -d
/blastdb/Proteins.new/<b>uniprot</b> -o test.out
[gcg_blastpgp] WARNING: Could not find index files for database
/blastdb/Proteins.new/trembl.101
[gcg_blastpgp] WARNING: Could not find index files for database
/blastdb/Proteins.new/trembl.102
...
[gcg_blastpgp] WARNING:  [000.000]  Could not find index files for
database /blastdb/Proteins.new/trembl.101
[gcg_blastpgp] WARNING:  [000.000]  Could not find index files for
database /blastdb/Proteins.new/trembl.102
...
[gcg_blastpgp] ERROR: ncbiapi [000.000]  SeqPortNew: lcl|20956
stop(379) >= len(117)
[gcg_blastpgp] ERROR: ncbiapi [000.000]  SeqPortNew: lcl|20956
stop(120) >= len(117)
...
Running the same comand with swissprot works ok:
$ /usr/users/gcg/linuxbin/gcgbin/pub/gcg_blastpgp -i pdb1a9x.seq -d
/blastdb/Proteins.new/<b>swissprot</b> -o test.out

How can this problem be resolved?
Thanks.

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[melvin-12]

Hi,
What version of Uniprot are you workin on?
The latest Uniprot is know to have undergone a format change & that
means,
the conventional programs working on it could fail.
-Peace

vadaner@... wrote:

> Hello,
> While running blastpgp on a newly downloaded UniProt database we get
> the following error:
>
> $ /usr/users/gcg/linuxbin/gcgbin/pub/gcg_blastpgp -i pdb1a9x.seq -d
> /blastdb/Proteins.new/<b>uniprot</b> -o test.out
> [gcg_blastpgp] WARNING: Could not find index files for database
> /blastdb/Proteins.new/trembl.101
> [gcg_blastpgp] WARNING: Could not find index files for database
> /blastdb/Proteins.new/trembl.102
> ...
> [gcg_blastpgp] WARNING:  [000.000]  Could not find index files for
> database /blastdb/Proteins.new/trembl.101
> [gcg_blastpgp] WARNING:  [000.000]  Could not find index files for
> database /blastdb/Proteins.new/trembl.102
> ...
> [gcg_blastpgp] ERROR: ncbiapi [000.000]  SeqPortNew: lcl|20956
> stop(379) >= len(117)
> [gcg_blastpgp] ERROR: ncbiapi [000.000]  SeqPortNew: lcl|20956
> stop(120) >= len(117)
> ...
> Running the same comand with swissprot works ok:
> $ /usr/users/gcg/linuxbin/gcgbin/pub/gcg_blastpgp -i pdb1a9x.seq -d
> /blastdb/Proteins.new/<b>swissprot</b> -o test.out
>
> How can this problem be resolved?
> Thanks.

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