[Bioperl-l] Bio::Index::Fastq - Interface for indexing (multiple) fastq files failure

Cook, Malcolm MEC at stowers.org
Wed Apr 7 11:25:05 EDT 2010


c.f. http://github.com/acr/screed
 
 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of KOVALIC, DAVID K [AG/1000]
Sent: Monday, April 05, 2010 1:28 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Bio::Index::Fastq - Interface for indexing (multiple) fastq files failure

Hi,

Using the example code for this module I get an error building an index
file:

		>index_fastq Run101_s11_test_index
100108_SOLEXA-02_0101_PE_61810AAXX/s_1_1_sequence.txt
		sdbm store returned -1, errno 22, key
"SOLEXA-02_0001:1:55:1110:290#0/1" at
/bli/lib/SunOS/perl5/site_perl/5.6.1/Bio/Index/Abstract.pm line 714, <FASTQ> line 30369077.

The code to build index file/retrieve sequences works on small test file but not the real data (fasyq file from single Illumina GAII lane). Here is the code for building the index.

Index_fastq:
		# Complete code for making an index for several
		# fastq files
		use Bio::Index::Fastq;
		use strict;

		unless (scalar @ARGV >= 2){die "ERROR index_fastq:
Usage: index_fastq <index file name> <(list of) fastq file(s) to index> \n\n"}

		my $Index_File_Name = shift;
		my $inx = Bio::Index::Fastq->new('-filename' => $Index_File_Name,'-write_flag' => 1);
		   $inx->make_index(@ARGV);

Any idea what the problem might be and how to fix it? Let me know if you have any insight. Thanks,

David



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