[Bioperl-l] bp_genbank2gff.pl giving errors when using file....

Gowthaman Ramasamy gowthaman.ramasamy at sbri.org
Tue Jul 7 17:59:41 UTC 2009

Hi All, 
I am trying to  use bp_genbank2gff.pl script to convert a locally downloaded genbank file. It is throwing stack errors. But, the script works beautifully when I use --accession option to download and convert.

Any suggestions? Thanks very much for checking this.

the command i use:
perl bp_genbank2gff.pl --stdout --file NC_004329.nb 

and i am getting the following exception message:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: EMBL stream with no ID. Not embl in my book
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.5/Bio/Root/Root.pm:359
STACK: Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.5/Bio/SeqIO/embl.pm:189
STACK: Bio::DB::GFF::Adaptor::biofetch::load_from_file /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi/Bio/DB/GFF/Adaptor/biofetch.pm:163
STACK: bp_genbank2gff.pl:274

Many thanks in advance,

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