[Bioperl-l] Fwd: Error while indexing whole genbank

guillermo gcarbajosa at cnio.es
Wed Nov 15 12:43:10 EST 2006


Hello,

I just indexed BCT without problems and now I am going to do it in  
parts, different indexes for each one, for PLN, PRI, ROD, etc. Anyways,  
I««l try to do it for the whole genbank and if it works I«ll let you  
know.

Thanks for the support,
Guille

Inicio mensaje reenviado:

> De: guillermo <gcarbajosa at cnio.es>
> Fecha: 14 de noviembre de 2006 11:39:41 GMT+01:00
> Para: bioperl-l at bioperl.org
> Asunto: Error  while indexing whole genbank
>
> Hello,
>
> I am trying to index the whole of genbank nucleotide (release number  
> 156, October 15 2006), with the script (which uses  
> Bio::Index::GenBank) that is attached at the end of this message the  
> process crashes  with this error message:
>
> sdbm store returned -1, errno 9, key "BF460808" at  
> /usr/local/lib/perl5/site_perl/5.8.8/Bio/Index/Abstract.pm line 714,  
> <GenBank> line 164732819.
>
> why could this be?
>
> Thanks,
> Guillermo
>
>
> #!/usr/local/bin/perl -w
>
> # Perl pragma to restrict unsafe constructs
> use strict;
>
> # Issue warnings about suspicious programming.
> use warnings;
>
> # Use the code module that contains BioPerl Services.
> use Bio::Index::GenBank; # Use to index GenBank file
> use Bio::SeqIO;
>
> # be prepare for command-line options/arguments
> use Getopt::Std;
>
> sub help {
> return<<"END_HELP";
> Description: Make index from GenBank database
> Usage:
>
> createGenBankIndex.pl -d {index file} -g {GenBank database}
> 	-d path and file name of index database
> 	-g GenBank database path
> 	
> END_HELP
>
> }
>
>
> BEGIN {
> 	
> 	# Determines the options with values from program
> 	use vars qw/$opt_d $opt_g/;
> 	
> 	# these are switches taking an argument (a value)
> 	my $switches = 'dg';
> 	
> 	# Get the switches
> 	getopt($switches);
> 	
> 	# If the user does not write nothing, skip to help
> 	unless (defined($opt_d) || defined($opt_g)){
> 		print help;
> 		exit 0;
> 	}
> 	
> }
>
> ####################################################################### 
> ########
> #
> # DESCRIPTION: The next program creates an BioPerl index aside GenBank  
> database.
> #
> # INPUT (BY CONSOLE): 	- (-d) Path where the Uniprot index is going to  
> store.
> #			- (-g) Path where GenBank database is located
> #
> # OUTPUT: 		- O => The program has finished sucessfully
> #			- 1 => Some of database files has not founded
> #			- 2 => There was an error while the process was running
> #
> # AUTHOR: José Manuel Rodríguez Carrasco -jmrc at cnb.uam.es- (INB-CNB)
> ####################################################################### 
> ########
>
>
> # Check if the path of GenBank database is able to read
> unless (-f $opt_g && -r $opt_g) {
>
> 	# The GenBank database has not been found
> 	print "Error of createGenBankIndex program: The GenBank database has  
> not been found\n";
> 	
> 	# Return an error
> 	exit 1;
> }
>
>
> # Store the database paths
> my @DBList = ($opt_g);
>
> # Create new instance to index file. It is used the option
> my $indexSW = Bio::Index::GenBank->new ('-filename' => $opt_d,
> 					'-write_flag' => 1);
>
> # Make the index
> my $numFiles = $indexSW->make_index(@DBList);
>
> # Check how many databases have been indexed
> if ($numFiles == 1) {
>
> 	# There has been not exist error.
> 	print "\nThe creation of GenBank index has been executed  
> successfully\n";
> 	exit 0;
> 	
>
> } else {
>
> 	# There has been exist an process error
> 	print "\nThere was a problem while the creation of GenBank index was  
> running\n";
> 	exit 2;
> }
>


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