[Bioperl-l] warning: Bio::Index::Fastq;

[Peter Cock]

I would guess there could be a problem with your FASTQ file,
since if I am reading the error correctly it has confused a
quality line (which happens to start with '@') with a read
identifier (lines which always start with '@').

Have you had problems with other tools reading this data?

What does this give - using grep to show the region around
the problem line:

grep -C 10 "^@@DDDDDFFFFFIIIDCBBBB"

Peter

On Mon, Mar 10, 2014 at 1:18 PM, EpiMAN <eh_mcb at yahoo.com> wrote:
> Hi,
>
> I want to index a fastq file and then extract the sequences by their IDs:
>
> I used the following code to make an index:
>
> perl index.pl index file.fastq
>
> ========================================
> #index.pl
> use strict;
> use warnings;
> use Bio::Index::Fastq;
>
>
> my $Index_File_Name = shift;
>
> my $inx = Bio::Index::Fastq->new('-filename'
> =>$Index_File_Name,'-write_flag'=>1);
> $inx->make_index(@ARGV);
> ===========
>
> I get a lot of warnings like:
> .
> .
> .
> --------------------- WARNING ---------------------
> MSG: overwriting a current value stored for
> @@DDDDDFFFFFIIIDCBBBB##############################################################################
> .
> .
> .
> .
>
>
>
>
>
>
>
>
>
>
>
>
> --
> View this message in context: http://bioperl.996286.n3.nabble.com/warning-Bio-Index-Fastq-tp17362.html
> Sent from the Bioperl-L mailing list archive at Nabble.com.
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