[Bioperl-l] bp_fetch.pl genbank example doesn't work anymore

Robert Buels rbuels at gmail.com
Thu Sep 13 14:42:08 EDT 2012


Sigh.

rob at x bioperl-live$ perl -I. scripts/*/bp_fetch.pl net::genbank:X47072
Sequence X47072 in Database genbank in net::genbank:X47072 is not 
loadable. Skipping.

Error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: id 'X47072' does not exist
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::DB::WebDBSeqI::get_Seq_by_id Bio/DB/WebDBSeqI.pm:167
STACK: scripts/index/bp_fetch.pl:307
-----------------------------------------------------------
Sequence X47072 in Database genbank in net::genbank:X47072 is not 
loadable. Skipping.

Error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: WebDBSeqI Request Error:
HTTP/1.1 400 Bad Request
Cache-Control: private
Connection: close
Date: Thu, 13 Sep 2012 18:40:49 GMT
Server: Apache
Content-Type: text/plain; charset=UTF-8
Access-Control-Allow-Origin: *
Client-Date: Thu, 13 Sep 2012 18:40:49 GMT
Client-Peer: 165.112.7.20:80
Client-Response-Num: 1
Client-Transfer-Encoding: chunked
NCBI-SID: 73BF4D7E05228B11_0006SID
Set-Cookie: ncbi_sid=73BF4D7E05228B11_0006SID; domain=.nih.gov; path=/; 
expires=Fri, 13 Sep 2013 18:40:49 GMT

Cannot process ID list: OUT OF RANGE. Parameter retstart=0 + 1 is 
greater than number of IDs supplied in request. Incoming request 
includes 0 IDs.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::DB::WebDBSeqI::_stream_request Bio/DB/WebDBSeqI.pm:773
STACK: Bio::DB::WebDBSeqI::get_seq_stream Bio/DB/WebDBSeqI.pm:467
STACK: Bio::DB::WebDBSeqI::get_Stream_by_id Bio/DB/WebDBSeqI.pm:288
STACK: Bio::DB::WebDBSeqI::get_Seq_by_id Bio/DB/WebDBSeqI.pm:158
STACK: scripts/index/bp_fetch.pl:307
-----------------------------------------------------------




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