<div dir="ltr">Hi Everyone,<div>    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.</div><div>I am just pasting few lines for example and an error message.</div><div>Would really appreciate your help.</div><div>





<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">use Bio::SeqIO;</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">use Bio::Seq::Quality;</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">$in = Bio::SeqIO->new(-file => "gunzip -c $ARGV[0]|", -format => 'fastq');<span class="gmail-Apple-converted-space">           </span></span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">while(my $seq = $in->next_seq){</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">      </span>my $id = $seq->id;</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">      </span>print "$id\n";</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">}</span></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><br></span></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">Error message:</span></p><p class="gmail-p1" style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">MSG: Could not read file 'gunzip -c com.fastq.gz|': No such file or directory</span></p><p class="gmail-p1" style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">STACK: Error::throw</span></p><p class="gmail-p1" style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">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</span></p><p class="gmail-p1" style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">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</span></p><p class="gmail-p1" style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">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</span></p><p class="gmail-p1" style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">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/<a href="http://fastq.pm:30">fastq.pm:30</a></span></p><p class="gmail-p1" style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">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</span></p><p class="gmail-p1" style="margin:0px;font:11px Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">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</span></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">













</span></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">STACK: testGZ.pl:5</span></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><br></span></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">Thanks</span></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">Shalu</span></p></div></div>