[Bioperl-l] Bio::Assembly::IO problems reading .ace files

[Chris Fields]

This seems similar to the 'too many open filehandles issue' documented  
here:

http://bugzilla.open-bio.org/show_bug.cgi?id=2320

It unfortunately is due to having an open DB_File for every contig,  
and is a problem with the Bio::Assembly implementation that isn't  
easily fixed.  Changing the open filehandle limit using ulimit is the  
only known fix:

ulimit -n 10000

chris

On Dec 3, 2007, at 6:49 PM, Smithies, Russell wrote:

> Hi all,
>
> It' trying to read .ace files but keep getting an error that I don't
> know the cause of.
> Really basic example code:
>
> 	#!/usr/local/bin/perl -w
>
> 	use lib "/data/home/smithiesr/bioperl-live";
> 	use Bio::Assembly::IO;
> 	use Data::Dumper;
>
> 	$ace = "CLP0001001240-cE15_20030319.ace";
>
> 	$io = new Bio::Assembly::IO(-file=>$ace,-format=>"ace");
> 	$assembly = $io->next_assembly;
>
> 	foreach $contig ($assembly->all_contigs) {
>      		print Dumper $contig;
> 	}
>
> Gives this error;
> 	[smithiesr at impala ace_phrap]$ perl bp_read_ace.pl
> 	Can't call method "get_consensus_sequence" on an undefined value
> at /data/home/smithiesr/bioperl-live/Bio/Assembly/IO/ace.pm line 170,
> <GEN0> line 42.
>
> Which relates to this bit in ace.pm:
> 	# Loading contig qualities... (Base Quality field)
> 	/^BQ/ && do {
> 	    my $consensus = $contigOBJ->get_consensus_sequence()->seq();
>
> Is this caused by a dud ace file or a problem with  
> Bio::Assembly::IO:ace
> or is the Contig object not getting created?
> Any ideas?
>
> Thanx,
>
> Russell Smithies
>
> Bioinformatics Software Developer
> T +64 3 489 9085
> E  russell.smithies at agresearch.co.nz
>
> Invermay  Research Centre
> Puddle Alley,
> Mosgiel,
> New Zealand
> T  +64 3 489 3809
> F  +64 3 489 9174
> www.agresearch.co.nz
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign