[Bioperl-l] reading gz fastq File

[shalu sharma]

Hi Everyone,
    So i am trying to work on gzip fastq files. In past my script used to
work fine. Now when i ran the same script it gives me an error.
I am just pasting few lines for example and an error message.
Would really appreciate your help.

use Bio::SeqIO;

use Bio::Seq::Quality;

$in = Bio::SeqIO->new(-file => "gunzip -c $ARGV[0]|", -format => 'fastq');


while(my $seq = $in->next_seq){

      my $id = $seq->id;

      print "$id\n";

}


Error message:

MSG: Could not read file 'gunzip -c com.fastq.gz|': No such file or
directory

STACK: Error::throw

STACK: Bio::Root::Root::throw
/usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/Root/Root.pm:447

STACK: Bio::Root::IO::_initialize_io
/usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/Root/IO.pm:268

STACK: Bio::SeqIO::_initialize
/usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/SeqIO.pm:513

STACK: Bio::SeqIO::fastq::_initialize
/usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/SeqIO/
fastq.pm:30

STACK: Bio::SeqIO::new
/usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/SeqIO.pm:389

STACK: Bio::SeqIO::new
/usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1/lib/perl5/site_perl/5.24.1/Bio/SeqIO.pm:435

STACK: testGZ.pl:5


Thanks

Shalu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/bioperl-l/attachments/20190225/d37707fe/attachment.html>